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Cybermidas - if you have a backup of your library prior to making the 'blunder' restore it. If you don't, make a mental note to do something about that once your current problems are resolved.
Otherwise - First do what PeterT suggests
Run Library Maintenance->Check Library. It runs in two stages, the first checks the internal integrity of the database, errors from it are very rare - I've never seen one.
The second optional stage compares the content of the database against the existence and content of the library subfolders (author and book). It is not uncommon for this stage to report anomalies, e.g. a Book record exists in the database but there's no corresponding book folder, an author folder exists for which there is no corresponding Author record in the database.
These anomalies should be resolved. They are often caused users using their file managers to change the folder names or contents, they can also be caused by abrupt hardware failures - power, video card etc
Added : btw: there's nothing a file manager can do that calibre can't do, apart from wreak havoc with your library. Equivalent to breaking into a library and moving the books and shelves around

Second do what theducks first suggested.
Use the optional Find Duplicates plugin to find the duplicates, if you add the Date column to the book list you should be able to easily identify the most recently added instance of duplicates - that's the one you probably want to remove.
In Preferences->Add Books there are settings relating to how duplicates are to be handled, you might want to review what you have there.
Added : actually - you should do something about backup now, back it up before undertaking the above repairs. Then if you make things worse you'll be able to start over.
BR