My guess is this is what I've had happen, in which case:
- if you delete an action from the action list and refresh, you should have a cleared action list
- if you go to a location and Flirt with X, you will unlock the associated sex action
- for the other vanished actions, you need to do whatever action unlocked them at least once (Repair Milking Station at the Farm before you can Use Milking Station, Work at the Cafe before you can Barista Training or anything, you might sometimes need to Scavenge before you can use the actions unlocked by Scavenge)
I don't know of any solution for the Undercity link though, and this might not help if you have the UI bug as well.