When changes are branch specific and should not be merged (back) to other branches, these changes should be discarded.

The following TFS command will discard changsets:

tf merge $/Project/SourceBranch $/Project/TargetBranch /discard /recursive /version:C10000~C10000

This example command discards pending merge changesets from SourceBranch to TargetBranch.
It discards changeset 10000. The version is a from ~ to, so you can discard multiple changesets at once.

When the command has finished, you still need to check in the merge.