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I know how Shedninja's ability, if put on the right Pokemon with the right set up, could be unstoppable; but I'm wondering if the game has something that will prevent the switch.

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I know that shedinja has wonder guard which stops all kinds of attacks but I don't really understand the question so can you explain it a Lil

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Best answer

Yes, certain abilities cannot be copied. This is due to reasons such as becoming overpowered (as you stated with Wonder Guard), being a forme change ability for formes other Pokémon don't have, or otherwise causing issues.

Note that all these can be copied using Ditto.

-Trace
-Forecast
-Flower Gift
-Battle Bond
-Comatose
-Power of Alchemy
-Receiver
-RKS System
-Disguise
-Schooling
-Shields Down
-Stance Change
-Illusion
-Imposter
-Wonder Guard
-Multitype
-Zen Mode

Some of these abilities cannot be copied, but still can be replaced with moves like Worry Seed or abilities like Mummy. They are marked with italics.

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edit: didn't notice the question edit, some of these don't apply to Skill Swap but apply to other ability copying moves, I can edit those out if wanted

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Wonder Guard can't be suppressed by Gastro Acid, Worry Seed, or Mummy?
So basically shedninja's ability can't be given to another pokemon(also someone changed what my actual question was but I can work with is)
That was directed at Lenny.  His answer seems to imply that you can't suppress Wonder Guard, so you can give Shedinja a different ability (such as Sturdy...).  My understanding was that you can move Wonder Guard around, but only after it has been suppressed (aka turned off, no longer functioning).  I was seeking clarification on that.