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.

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