Cover will be deleted automatically

Add cover by file and afterwards click in any tag field (album, year - equal if filled or blank).
If you do not have saved the cover first, it will be deleted if you click in any other tag field.... try it
Adding a cover by freedb, MusicBrainz or from wherever.... does not fail.

Actually, no modified data in the tag panel is saved unless you say so explicitly.
See e.g. here:

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