This is a known issue.
I remember reading that once that when you ask tanker permission to re-fuel you actually change the definition of the flight lead to the tanker (or some other technical explanation of some sort). Due to that, if you give your flight a command during tanker communication you create an exception that keeps the tanker as flight lead (due to game “privileges” bug) and then you basically lose control of your flight.
I’m probably mixing up the terminologies but I’m 99% sure that’s the main issue.
I tried looking up the thread after posting and came up short. My best suggestion is trying to re-generate the bug to confirm.
Try refueling and not give any wing/element/flight commands during refueling (meaning until #4 has been fully disconnected) and see if they come back.
Then try refueling again giving a command and see if they stick.
Hope this helps,
MadBafla