I think I've experienced a similar issue a couple of times, and although it may line up with other progression issues people have been having, I figured I'd record it just in case.
The first time I saw this was when I acquired AD1; I'd previously had my Kyra die during Black Fang's Dungeon, but had finished the scenario with Merisiel. Once I acquired AD1 and went back to play the scenario again, however, all progression vanished, and I had to replay the entire base set to gain access to AD1. My speculation at the time was that it was somehow related to gaining access to the next set of scenarios.
Everything seemed fine when I went back through, but when I acquired AD2, even though I didn't have some characters who had access and some who didn't, progress was again reset back to base level. As others (Hannibal, I think) have said, it's the "party" progress that's wiped; I still have access to higher difficulty levels. I wiped my party again, and ran through the scenarios again.
I wasn't thinking that I would encounter anything unusual as I approached the end of AD2, since there wasn't an AD3 available, but I just finished the last scenario, and I'm stuck at rebuilding decks. I'm presented the cards available to me based on the adventure, but with the card feats the characters just got, I'm unable to give them all the cards they need, and the "advance" button never enables. Specifically, I chose a spell for Ezren, a blessing for Meri, and a spell for Kyra. Ezren's got plenty of spells, but banished an ally, and we didn't get any, so he has no choices. Kyra needs a spell, but interestingly, even if I ditch one from Ezren, I have difficulty moving that into Kyra's list. To be fair, I believe this is a separate issue, but because of the timing, I'm including it here.