Thanks guys got my Genesis collection sorted in about an hour. Basically I updated everything through Genesis platform first. Then I changed all the games without a gdb id to Mega Drive. Then ran the update process for the Mega Drive games. That took care of about half of those games and then I manually updated the rest.
Often when a gdb id can't be found, when you go to search for the game manually 99% of the time the first search suggestion is correct. One feature that would be nice is to be able to toggle that if an exact match is not found, then the first search result should be used