I am actually aware of this interaction and I am unsure whether it should be changed or just communicated better in-game.
The upgrade effect works as follows:
1. Apply changes prescribed by upgrade (in this case, +1 more piety)
2. 'Preserve' card to deck, saving all the changes it has received during stage so far, including the upgrade. For example, if you would play Strategy, then Rune of Perfection, the max Persist count on Pray will increase permanently. (As a side note, this preservation effect make runes much more powerful than they seem. Consider using them with Secret Technique for example, or even Supreme Edict + Avatar of Virtue).
Since the card stores 'current' and 'max' persist counts separately, it is possible to modify it so that is does not have the specific 'downgrade' effect you encountered, but then the positive version of it will be also lost, which is a pity IMO. Alternatively, I can separate 'upgrade' and 'preserve' effects in card description to make it more evident. I would like to hear your opinion on this.
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