You mean the Season 1 saves right? That one is on my list to fix. Looking at the code I've written, the second season application always checks for a Season 1 save to be present, even if you've played episodes of the second season already and have deleted the first season saves for some reason. I'm going to broaden the check to include the detection of Season 2 saves.
I played up to v20 without a problem, but v21 gave me the no saves detected screen.
I fixed that by first deleting the saves in the appdata folder for both S1 and S2.
Then I copied my S1 saves to the S2(v21) folder. Basically my old and new saves merged.
That worked.
I'm replaying now and on this run I copied my S1 saves to the S2(v21) folder before even starting S2(v21) and this time I didn't have any problems at all. I'm not sure where to problem is but I appreciate you checking if something got messed up somewhere.