Only change Publication Flags that Users have Permissions for

[Masterjun3]

Resolves #1767 .
With permissions involved we can't just clear the whole list and then set those selected. We need to only remove those the user can edit, and then only set those the user can edit and has selected.

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Also, it seems these previous two lines were doing the exact same thing. This stuff looks redundant.

publication.PublicationFlags.Clear();

_db.PublicationFlags.RemoveRange(
			_db.PublicationFlags.Where(pf => pf.PublicationId == publication.Id));

And this is still being done for the Publication Tags (instead of the Flags).