I am actually having this problem right now.
So I have not really played much with retail lots etc. but I decided to get a vet. At first I thought it might be a weird sort of feature that you had to spend the points as soon as you got them as mine had disappeared the first time I revisited the lot (why did I think that?)
I then noticed I had to purchase a perk I had already purchased and started getting confused. Surely it wasn't meant to be like this!
However I think I have found the trigger. (at least in my game)
Whenever I move out a young adult sim, my points reset and my perks disappear. I haven't tried with anyone else than young adult so it might be with all ages.
