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Describe the Bug:
When Protean Hydra is dealt enough damage to remove all its counters (but doesn't die do to outside pumping) at end of turn it gets the wrong number of counters (ex. lost 16 counters and got 8 back at end of turn)

Also seen if it is dealt enough damage to remove all of its counters (but not die) and is then dealt damage again (removing zero counters) at end of turn it doesn't get any counters.

Which card did behave improperly ?
Protean Hydra

Which update are you using?(date,name)Which type(Duel,Gauntlet,Sealed Deck)
Manalink 2014/9/28: Conspiracy for the recoding of M15 minipatch 3,duel

What exactly should be the correct behavior/interaction ?
Should get 2x as many counters as were lost

Are any other cards possibly affected by this bug ?
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I confirm this 1st bug with your savegame,I don't know if it has to do with Spidersilk Armor & +0/+1 that gives to Protean Hydra.
I tested with Gaea's Anthem and Protean Hydra loosing all it's counters and the # of counters that were added were correctly double.

About 2nd bug I confirm it,it seems it only remembers if the last damage removed any counters to double them if the same turn all counters were removed from hydra and then it prevented more damage without any counters to be removed,instead of tracking all counters removed this turn from Protean Hydra to double them.

Fixed the second bug in b7b5c34
For the other, is some kind of strange interaction...

This seems fixed/closed.