Recount on the TS has never been thought through, mostly because the concept is completely meaningless IMO. Right now traditional GEMS recount doesn't play well at all with TS. When you unset-for-election to setup the recount race set, you end up blowing away all your AVTS floppies (the version changes) and upload fails. I hacked around this for Jeff Hintz once by giving him a GEMS that ignores the upload version. I suppose that is SOP for the time being.
I have asked several times for a coherent explanation as to how recount should work for TS.
Its the whole ballot.
I spose, but what would be the point? I mean, if you were recounting paper ballots all the races would still be marked.