I was able to get around this by deleting the stuck story save and starting a new story with the freed up experienced characters. Everything seemed to be unlocked as it was in the old save. For Local Heroes specifically I tackled it solo with only the character that needed the completion. That seemed to go fine and I was able to continue on with a party of three afterwards. Though, I haven't tried replaying Local Heroes with a full evenly progressed party yet.
EDIT: Just tried a party of 2 and no issues.
