diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bc17df8d27..3569699b92 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -58,7 +58,7 @@ repos:
       # auto format Python codes within docstrings
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.7
+    rev: v0.4.8
     hooks:
       # lint & attempt to correct failures (e.g. pyupgrade)
       - id: ruff
diff --git a/conda_build/build.py b/conda_build/build.py
index 9ee91811eb..3f7dc0470a 100644
--- a/conda_build/build.py
+++ b/conda_build/build.py
@@ -1753,13 +1753,16 @@ def bundle_conda(
                     output["script"],
                     args[0],
                 )
-            if "system32" in args[0] and "bash" in args[0]:
-                print(
-                    "ERROR :: WSL bash.exe detected, this will not work (PRs welcome!). Please\n"
-                    "         use MSYS2 packages. Add `m2-base` and more (depending on what your"
-                    "         script needs) to `requirements/build` instead."
+            if (
+                # WSL bash is always the same path, it is an alias to the default
+                # distribution as configured by the user
+                on_win and Path("C:\\Windows\\System32\\bash.exe").samefile(args[0])
+            ):
+                raise CondaBuildUserError(
+                    "WSL bash.exe is not supported. Please use MSYS2 packages. Add "
+                    "`m2-base` and more (depending on what your script needs) to "
+                    "`requirements/build` instead."
                 )
-                sys.exit(1)
         else:
             args = interpreter.split(" ")
 
@@ -4073,11 +4076,11 @@ def handle_pypi_upload(wheels, config):
             try:
                 utils.check_call_env(args + [f])
             except:
-                utils.get_logger(__name__).warn(
+                utils.get_logger(__name__).warning(
                     "wheel upload failed - is twine installed?"
                     "  Is this package registered?"
                 )
-                utils.get_logger(__name__).warn(f"Wheel file left in {f}")
+                utils.get_logger(__name__).warning(f"Wheel file left in {f}")
 
     else:
         print(f"anaconda_upload is not set.  Not uploading wheels: {wheels}")
diff --git a/conda_build/inspect_pkg.py b/conda_build/inspect_pkg.py
index 43fc401551..5747f3a7b8 100644
--- a/conda_build/inspect_pkg.py
+++ b/conda_build/inspect_pkg.py
@@ -258,7 +258,7 @@ def inspect_linkages(
                 if relative:
                     precs = list(which_package(relative, prefix))
                     if len(precs) > 1:
-                        get_logger(__name__).warn(
+                        get_logger(__name__).warning(
                             "Warning: %s comes from multiple packages: %s",
                             path,
                             comma_join(map(str, precs)),
diff --git a/conda_build/metadata.py b/conda_build/metadata.py
index 7305c62340..8baf0cf066 100644
--- a/conda_build/metadata.py
+++ b/conda_build/metadata.py
@@ -199,7 +199,7 @@ def get_selectors(config: Config) -> dict[str, bool]:
     if not np:
         np = defaults["numpy"]
         if config.verbose:
-            utils.get_logger(__name__).warn(
+            utils.get_logger(__name__).warning(
                 "No numpy version specified in conda_build_config.yaml.  "
                 "Falling back to default numpy value of {}".format(defaults["numpy"])
             )
@@ -998,7 +998,9 @@ def _toposort_outputs(output_tuples: list[OutputTuple]) -> list[OutputTuple]:
             non_conda_outputs.append(output_tuple)
         else:
             # TODO: is it even possible to get here? and if so should we silently ignore or error?
-            utils.get_logger(__name__).warn("Found an output without a name, skipping")
+            utils.get_logger(__name__).warning(
+                "Found an output without a name, skipping"
+            )
 
     # Iterate over conda packages, creating a mapping of package names to their
     # dependencies to be used in toposort
@@ -2329,7 +2331,7 @@ def extract_single_output_text(
             output = output_matches[output_index] if output_matches else ""
         except ValueError:
             if not self.path and self.meta.get("extra", {}).get("parent_recipe"):
-                utils.get_logger(__name__).warn(
+                utils.get_logger(__name__).warning(
                     f"Didn't match any output in raw metadata.  Target value was: {output_name}"
                 )
                 output = ""
diff --git a/conda_build/os_utils/liefldd.py b/conda_build/os_utils/liefldd.py
index 3823ce4a9d..b474a4897a 100644
--- a/conda_build/os_utils/liefldd.py
+++ b/conda_build/os_utils/liefldd.py
@@ -1174,6 +1174,10 @@ def __call__(self, *args, **kw):
                         if not data:
                             break
                         sha1.update(data)
+                # update with file name, if its a different
+                # file with the same contents, we don't want
+                # to treat it as cached
+                sha1.update(os.path.realpath(arg).encode("utf-8"))
                 arg = sha1.hexdigest()
             if isinstance(arg, list):
                 newargs.append(tuple(arg))
diff --git a/conda_build/utils.py b/conda_build/utils.py
index 17d1c1f031..e5e8d9c8c2 100644
--- a/conda_build/utils.py
+++ b/conda_build/utils.py
@@ -1318,7 +1318,7 @@ def find_recipe(path: str) -> str:
 
     metas = [m for m in VALID_METAS if os.path.isfile(os.path.join(path, m))]
     if len(metas) == 1:
-        get_logger(__name__).warn(
+        get_logger(__name__).warning(
             "Multiple meta files found. "
             f"The {metas[0]} file in the base directory ({path}) "
             "will be used."
diff --git a/news/4821-include-file-hash b/news/4821-include-file-hash
new file mode 100644
index 0000000000..fa155e4ac3
--- /dev/null
+++ b/news/4821-include-file-hash
@@ -0,0 +1,19 @@
+### Enhancements
+
+* <news item>
+
+### Bug fixes
+
+* Include file path in addition to the content when generating the file hash to avoid unwanted caching during linkage analysis. (#4821)
+
+### Deprecations
+
+* <news item>
+
+### Docs
+
+* <news item>
+
+### Other
+
+* <news item>
diff --git a/tests/test-recipes/split-packages/_test-file-hash/build.sh b/tests/test-recipes/split-packages/_test-file-hash/build.sh
new file mode 100644
index 0000000000..5cf09c5b51
--- /dev/null
+++ b/tests/test-recipes/split-packages/_test-file-hash/build.sh
@@ -0,0 +1,8 @@
+echo "int main() {}" > main.c
+mkdir -p $PREFIX/bin
+$CC main.c -o $PREFIX/bin/_file_hash
+
+echo "int foo() {return 2;}" > foo.c
+echo "int foo(); int bar() {return foo()*2;}" > bar.c
+$CC -shared foo.c -o libupstream.so
+$CC -shared bar.c -o libdownstream.so -L$PWD -lupstream '-Wl,-rpath,$ORIGIN'
diff --git a/tests/test-recipes/split-packages/_test-file-hash/conda_build_config.yaml b/tests/test-recipes/split-packages/_test-file-hash/conda_build_config.yaml
new file mode 100644
index 0000000000..5b99fedac2
--- /dev/null
+++ b/tests/test-recipes/split-packages/_test-file-hash/conda_build_config.yaml
@@ -0,0 +1,3 @@
+python:
+- 3.10
+- 3.11
diff --git a/tests/test-recipes/split-packages/_test-file-hash/install-py.sh b/tests/test-recipes/split-packages/_test-file-hash/install-py.sh
new file mode 100644
index 0000000000..7a37b6050b
--- /dev/null
+++ b/tests/test-recipes/split-packages/_test-file-hash/install-py.sh
@@ -0,0 +1,4 @@
+mkdir -p $SP_DIR/_py_file_hash
+cp libdownstream.so $SP_DIR/_py_file_hash/
+cp libupstream.so $SP_DIR/_py_file_hash/
+
diff --git a/tests/test-recipes/split-packages/_test-file-hash/meta.yaml b/tests/test-recipes/split-packages/_test-file-hash/meta.yaml
new file mode 100644
index 0000000000..db0c9a89d1
--- /dev/null
+++ b/tests/test-recipes/split-packages/_test-file-hash/meta.yaml
@@ -0,0 +1,30 @@
+package:
+  name: _file_hash-split
+  version: 0.0.1
+
+build:
+  number: 0
+  skip: True  # [not linux64]
+  error_overlinking: true
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+  host:
+  run:
+
+outputs:
+  - name: py-file-hash
+    script: install-py.sh
+    requirements:
+      build:
+        - {{ compiler('c') }}
+      host:
+        - python
+      run:
+        - python
+
+  - name: _file_hash
+    requirements:
+      build:
+        - {{ compiler('c') }}
diff --git a/tests/test_build.py b/tests/test_build.py
index af5abb0f70..f1a9f11736 100644
--- a/tests/test_build.py
+++ b/tests/test_build.py
@@ -15,6 +15,7 @@
 from typing import TYPE_CHECKING
 
 import pytest
+from conda.common.compat import on_win
 
 from conda_build import api, build
 from conda_build.exceptions import CondaBuildUserError
@@ -22,6 +23,8 @@
 from .utils import get_noarch_python_meta, metadata_dir
 
 if TYPE_CHECKING:
+    from pytest_mock import MockerFixture
+
     from conda_build.metadata import MetaData
 
 
@@ -345,3 +348,24 @@ def test_copy_readme(testing_metadata: MetaData, readme: str):
     Path(testing_metadata.config.work_dir, readme).touch()
     build.copy_readme(testing_metadata)
     assert Path(testing_metadata.config.info_dir, readme).exists()
+
+
+@pytest.mark.skipif(not on_win, reason="WSL is only on Windows")
+def test_wsl_unsupported(
+    testing_metadata: MetaData,
+    mocker: MockerFixture,
+    tmp_path: Path,
+):
+    mocker.patch(
+        "conda_build.os_utils.external.find_executable",
+        return_value="C:\\Windows\\System32\\bash.exe",
+    )
+
+    (script := tmp_path / "install.sh").touch()
+    with pytest.raises(CondaBuildUserError):
+        build.bundle_conda(
+            output={"script": script},
+            metadata=testing_metadata,
+            env={},
+            stats={},
+        )
diff --git a/tests/test_post.py b/tests/test_post.py
index 97ef1448fc..eb2672218a 100644
--- a/tests/test_post.py
+++ b/tests/test_post.py
@@ -18,7 +18,7 @@
     package_has_file,
 )
 
-from .utils import add_mangling, metadata_dir
+from .utils import add_mangling, metadata_dir, subpackage_path
 
 
 @pytest.mark.skipif(
@@ -156,6 +156,26 @@ def test_menuinst_validation_fails_bad_json(testing_config, caplog, tmp_path):
     assert "JSONDecodeError" in captured_text
 
 
+def test_file_hash(testing_config, caplog, tmp_path):
+    "check that the post-link check caching takes the file path into consideration"
+    recipe = Path(subpackage_path, "_test-file-hash")
+    recipe_tmp = tmp_path / "test-file-hash"
+    shutil.copytree(recipe, recipe_tmp)
+
+    variants = {"python": ["3.11", "3.12"]}
+    testing_config.ignore_system_config = True
+    testing_config.activate = True
+
+    with caplog.at_level(logging.INFO):
+        api.build(
+            str(recipe_tmp),
+            config=testing_config,
+            notest=True,
+            variants=variants,
+            activate=True,
+        )
+
+
 @pytest.mark.skipif(on_win, reason="rpath fixup not done on Windows.")
 def test_rpath_symlink(mocker, testing_config):
     if on_linux: