If calibre is crashing when you try to perform maintenance, then something is wrong, it shouldn't do that. It sounds like something is wrong with the new database as well. Can you describe the steps you took to get this problem?
Adding the books again will create a new entry, but if the books don't have an entry at the moment, you will end up with one entry, I'd think. It won't however, overwrite the files in the library. calibre uses an id number included in the filename that will never be reused to make sure each book record is unique.
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