Well, I have been fighting with Domain licenses since I have been on R80.10 (first step into R80.x) but currently I found a way that seems to work. Local licenses need to be removed from GAIA WebUI or CLI. When you collected the license into the SmartUpdate you need to just do a get license to get rid of it.
All Doman blade licenses are licensed to the IP of the MDS itself and added to the repository, once you add the license they will be added. When you add the file twice, it will just add them to the repository twice and you can use them....
Somewhere around jumbo take 73 there were some updates to the License handling and this improved a bit, but not much, before I could not remove any license from a domain and ended up with 5 Domain licenses on a domain. Finally with GuiDBedit (under TAC scrutiny) I was able to make some changes that allowed me to finally remove the licenses from the domains and start over again and properly assign the right license to each domain.
Regards, Maarten