Switching versions of #amethyst resulted in losing all the hashtags and locations I was following.
Damnit.
Luckily the hashtags are easy to fix as I keep them in my profile.
Had to go through my previous geotagged posts to recover the locations.
Discussion
Humm... Very strange. Are you sure this wasn't another client deleting them? We save them together with the contact list. So if your follows are kept but not the hashtags, then it's probably some other client deleting things they don't support yet. Usually that happens when you follow or unfollow, or adjust your relay settings in another client.