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You can manage & track your card collection and decks once you create an account and login.
Once an Upgrade is legally put into a slot, it stays there, even if the ability that allowed it to be upgraded in the first place no longer applies. In your example, you could keep Mining Pick in Predakings Armor slot. Upgrades that are on characters that combine into Combiners are considered to stay in their slots, even though those slots now belong to the Combiner.