The message is because you now have an empty Library, but calibre does not know it (says you have a Mobi file for that book)
First Make a BACKUP of the current (mostly empty) Library folder, just in case thing go belly up.
->Not tested<- be sure to have a backup
Preferences Adding Books: Auto Merge Books:Overwrite Existing Duplicate formats (We know they don't really exist)
APPLY
Now Add your books using the Add Books Icon: <Pick the appropriate choice> You can do this in small steps.
IMHO do a few, and see if the results for those please you
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