There are several ways to handle this, but first you may want to make a backup of your calibre library, to avoid loosing books or data.
One way is to use calibre to move the library to a new folder. Then calibre will leave behind the books it has lost track of. You can examine them and add the ones you don't already have in the library. You may already have another copy of the books in the library.
Another way, that may be faster, is to delete the database file, metadata.db, and have calibre recreate it from the library. The metadata should be backed up in OPF-files. (You might just rename the database file to metadata.bak to test this quickly.) You might end up with duplicate books...
The reason why this happened can be that you had some cloud sync software active while running calibre. Or did a restore of a backup to the same place as an existing calibre library. Or restored just an old metadata.db, and not the books at the same time. Or you have accessed the library from another computer, with another operating system that has different case sensitivity. Or something else...
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