mm0,
I have the same setup. When I added the 2nd HD Homerun Duel, I didn't rescan, I just checked the Television setting to make sure the other 2 tuners were recognized (and they were). I tried recording 3 shows and watch'd a 4th and all was well.
I would think the only reason to scan for channels would depend on how you have it setup.
I have 2 antenns (1 UHV and 1 VHF) the combine and go into a powered 2-port amp. The output of the each port on the amp goes to each HD HomeRun. Therefore, sense the antennas are in the same orientation, I didn't see the need to re-scan.
I live in Mission Viejo, CA (about half way between Los Angeles and San Diego), I could have one antenna pointed to LA and the other to SD, if I did that, I would re-scan to pickup the SD channels, however since the channels would be mostly duplicated I saw no reason to do that.