If you set a patch to "do not scan" and it gets changed a bit (by our content team), then - yes - we wouldn't change that. We'd still download the new content, bump the revision up - but the status of the vulnerability (i.e - do / do not scan) should be mantained.
HOWEVER ... if the patch needs to be re-released by the vendor (i.e. "MS12-345v2") then that's a *NEW* vulnerability definition alltogether effectively, and you might run afoul of it.
Hope that helps?