After hp was reverted it seems only my chanseys are affected.

Yes, this seems to be a fairly common problem.

It appears to only affect Chansey and Blissey - why just those, I'm not sure, but it might have something to do with the fact that they were hardest hit by the Defense/HP balance update.

It seems to be because they have a bug where changes to the stats leave mons with less than full hp. When they implemented the changes, almost everything got a higher hp and was at less than full. Blissey and Chansey are the only two species that have higher hp with the old formula, so when they reverted, those two ended up missing hp instead.