We resolved this, but maybe not in a way that will be repeatable for you.
Firstly, we used the commandlet to do the migration. Which did do a lot of work, but it seemed incomplete. We ended up with old and new assets around for some reason and had to do a bunch of cleanup by hand.
But a larger problem was that we had already put stuff into soundbanks (before event-based packagin existed). We didn't remove those soundbanks before doing the migrate, so they also got migrated. Which sort of defeats the purpose of the event based packaging. So, we unbanked everything. This is painful because every AkEvent asset has its bank stored in it, so one needs to modify all the events. (We used the matrix editor to do this. It's not hard, but there are a lot of files to check out/in for a large project like ours.) This seemed to fix a lot of the loading issues, but we still sometimes had sounds fail to play.
To "fix" that, basically, we cleared the sound cache and forced asset syncing several times and in various orders and combinations. Eventually, it seemed to work.
Sorry that we never found the main culprit. I think it was a combination of the soundbanks existing ahead of time, and the commandlet not working 100%.