I do not know what is broken with your system... Delete Permissions?
A number of us use "intake" type Libraries, where we clean and polish before moving (using Copy To Library: Delete) to the Main Library. Mine is clean (no strays visible inside the Library Folder) and I do not run the Library Maintenance on it very often.
Even when I went against the recommendations and my Calibre used for Intake was on a different PC (intake Library was a network share on the Main PC), all I saw was the GUI, (Edit Metadata) window would NOT get destroyed at the end of the edit. The metadata was saved just fine, Books moved and deleted... Even on a Network share.
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