[taming]

With KoBo WiFi, there should be no need to replace the sqlite Db. Just do a factory reset.

For Kobo-1, doing a replacement of the sqlite, images, AND kepub folders (do all three) will give you a clean start. If you have a corrupted Db, this is the way to go. See the sticky on sqlite replacement. You will end up with the preloaded books in kepub files, rather than in the sqlite Db.

It doesn't sound like you have any Db issues, so unless you value things like having the dictionary working with the preloads (only happens when they are kepub), then a factory reset should be good enough.

If Calibre sideloaded books remain on the reader (it's been awhile, so I don't remember), they may work after your first processing cycle, or you may have to delete the book folders Calibre creates on the Kobo and reload from scratch.

Then you can reload through Calibre or ADE--your choice.

If you buy books from multiple sources, you should be fine with ADE as long as you are using the same ADE account, and as long as they are all using the same flavour of ADE DRM (as do Sony and Kobo).Kobo does not work with the Nook or iBook ePUB DRM at all. Some people strip DRM if they are, for some reason, using two different ADE accounts or other formats.