What happens to counters when they are covered by another card?

Anytime a card with a counter on it (not including Storage Bombs in Hangars) is covered by another card (Malfunction, Armor upgrade) the counters dissapear and do not return. Here is a list of the cards that have counters and how they interact:

Torch Pipe: If Malfunction or an armor upgrade is played on Torch Pipe but then returns to an active Torch Pipe the counter resets back to +1.

Gears of Alvidon: If Malfunction or an armor upgrade is played on Gears of Alvidon but then returns to an active Gears of Alvidon the counter resets back to +1.

Thunder Shield: If Malfunction or another shoulder armor is played on Thunder Shield but then returns to an active Thunder Shield the ammo counters will be empty.

Refuge Laser: If Malfunction or another shoulder armor is played on Refuge Laser but then returns to an active Thunder Shield the ammo counters will be empty.

Gem Blastercon: If Malfunction or another armor is played on Gem Blastercon but then returns to an active Gem Blastercon the armor would again start at its +6 attack.

Destroyer Sky: If another pilot is played over Destroyer Sky, and then that pilot is removed returning Destroyer Sky to your active pilot, she would have zero attacks remaining (regardless of how many attacks she has made).

Spor Conductor: If Malfunction or an armor upgrade is played on Spor Conductor but then returns to an active Spor Conductor the counter resets back to +2.