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I did the same thing when i decided to share a portion of my library as mobi. I just used the save to disk feature and save them all as mobi with the other things i prefer like metadata perhaps or not. That was after i had made sure they were all converted.
You also wouldn't have to do file separation.
*Or you could do a search for just .epub but then you wouldn't be able to carry along meta data info.
You could then if you wanted rename the library in my documents and import into a new blank or try that multiple library feature which i haven't yet.
You would be surprised how fast they import back in when in a uniform file / naming structure.
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