UPDATE: Played a game and now I have all my perks.
2 of my perks have gone missing. I know this because I always keep 29 perks, and I'm currently sitting at 27. One of them was definitely the Medic perk that I just rolled last night. Interestingly, it's still equipped on Vanessa but not LaChappa.
Vanessa with the perk equipped: http://steamcommunity.com/sharedfiles/filedetails/?id=970229966
Perk Inventory with it missing: http://steamcommunity.com/sharedfiles/filedetails/?id=970230018
LaChappa with the perk missing: http://steamcommunity.com/sharedfiles/filedetails/?id=970230068
I'm not sure what other perk went missing because I wasn't using it. If it helps, I rolled a rare Medic perk last night and sold my old Uncommon perk.