I don't understand why you would expect to change an assembly by removing a part from it and yet not want it marked as being "Locally Modified". And when you move a part from an assembly to the root level, it has also been modified.
There is a workaround. There is a "goody" called "DB Dialog" that has an option where you can change the "Modified" status on a part or assembly so that they are not marked as being modified even when they have been modified.
What you request is actually a "user misunderstanding".
Moving a part from one assembly to another assembly is a modification of both assemblies - you are changing the "structure" of both assemblies,
but you are not changing the part itself.
Using the "DB Dialog" should be limited to exceptional cases only (e.g. to "unlock" a part that has been reserved by a person who has left the Company).
In the given case, everything is working as designed - so I recommend to use the system "as designed".
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