[Tarana]

Try it on 10 books first. See how it works. Once you have 20 books converting the way you want them to, then duplicate the library and convert that duplicate to a single format. MOST books will convert the way you want, but formatting in the original may prevent that occasionally. You will likely have to run the computer overnight.

I did this for my late sister several years ago - converted my library to a duplicate in mobi format only. Some of the books came up with blank lines between lines. I had to use the editor to fix that.

edited to add: I should add that if you go from say EPUB to MOBI, this works. I don't know if it will work if you have Epub to Epub. Again, 10 books at a time to see what works.