fix(SHS-6113): Exception on duplicate nodes being cleaned up

[joegl]

Summary

Fix for the duplicate node database update failure.
$permissions is sometimes not an array and fails when being ran through array_unique() (this is possibly due to the per_node setting being enabled).

Urgency

High

[joegl]

I ran this on the Economics site locally and it worked:

>  [notice] Update started: su_humsci_profile_update_9724
>  [notice] Update completed: su_humsci_profile_update_9724
>  [notice] Update started: su_humsci_profile_update_9725
>  [notice] Update completed: su_humsci_profile_update_9725
>  [notice] Update started: su_humsci_profile_update_9726
>  [notice] Update completed: su_humsci_profile_update_9726

I'm going to merge this one.