The first thing you mentioned sounds like it might be a bug. I'll need to investigate that. Sorry about the annoyance, there!
Continuing into the third part, whenever it releases, will work much the same as continuing into the second part from the first did. Each new version will read from the same save data location as the current version (%localappdata%), so all of your old saves will still be visible-- assuming they weren't deleted, and that you're using the same device, that is. Just hang onto your cleared saves and let the magic of mildly clever programming take care of the rest!