Seems the Boff Skill resetting issue from before Season 11 has returned (can't find any pre-existing threads for post season 11 on it). Thought at first it was me and/or just a one off reset with the underlying season 11 changes, but it seems to be persisting.
Haven't nailed down a repro case yet I'm afraid (so it may or may not be the same cause as pre-season 11), but seems to happen after changing ships around (particular when claiming/dismissing ships, adjusting applied boff skills), however bug doesn't seem to affect all Boff's and ship specific allocated skills don't change. As such it's most noticeable when going to a ground map with a boff and all the skills are set back to defaults which presumably the first unlocked skill at the top data table.
If I can get some more solid info I'll update the thread, if anyone else is experiencing this and can provide some helpful debug info please feel free to input it.