[Adoby]

When you work with big amounts of files and data like this, it is a good idea to make backups now and then. In your case copy the whole library to some other hard drive. Then, if/when there are problems you only have to restore the last working backup, and don't have to start over from the beginning.

Also I would suggest that it is a bad idea to add everything to calibre, and create a huge library full of junk and duplicates. I don't think you'll ever sort it out. Even if calibre can handle all the books, everything will be slow and sorts and searches and updates and changes takes a looong time. And most likely you spend a lot of that time on books you will delete later.

Instead add just a few books, 20-50, perhaps books you want to read soon, or books that you know are in a good state. And fix them so they are in a good or even perfect state with nice covers, complete metadata, tags, normalized author names, correct series and converted to the format(s) you need and safely backuped. Then add a new batch. Preferably the best and most interesting books first. Rinse and repeat. I believe that this actually will be as fast, since I suspect that you'll never finish, and you'll at least have a nice growing library as you work, instead of an embarrassing ugly heap of junk with a few nice nuggets in it, here and there.

You may also use more than one library. For instance one for fiction and one for non-fiction.