RaftTombstoneKey currently resides in the replicated range-local key space. This means that it will be included in snapshots and was being included (incorrectly) in consistency checks. #12131 added a hack to not include RaftTombstoneKey in consistency checks, but the real fix is to make it an unreplicated key.
Note that RaftTombstoneKey is special in that it is only supposed to exist if there is no corresponding replica data.
A migration would have to perform a one time loop over all of the tombstone keys for a store similar to what is done in Store.IterateRangeDescriptors.