@please55 - Kovid wrote "Automerge does not move files to trash." Which implies that any files replaced by the Automerge operation are hard deleted.
He then wrote " Only deleting does that," I interpret that as meaning "Only Removing does that", i.e. a user initiated delete of a book from a library.
Finally he wrote "Auto-merge is off by default for a reason." My emphasis. As you've found out turning it on can result in data loss, that's why it's default setting is off.
If you turn Add Books->Automerge... off, calibre will pop a dialogue if it detects a book already exists with the same title as the one its about to add, the dialogue has several buttons as to what to do about it.
I suggest you save the FR version somewhere, restore the lost EN version from backup and then decide on you want to do with the FR version.
BR
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