I tried the approach of adding more roms using the tools-> import approach, and I think it still created some duplicates.
For instance, I now see two copies of 'wonder boy' for genesis; one with region 'Japan' and one 'North America, Europe'. Looking at each more closely, one is actually combining 'brazil/japan', and the other, 'NorthAmerica Europe/ Brazil'. I think this happened because I added a brazil version, but I need to try and replicate to be sure.
Even still, maybe we could just have an option that scans selected games and combines them? That function seems to work really well during initial import, and I get one entry, labelled as the NorthAmerica region, but then it combines all other regions into that one. There is an option, 'consolidate roms', but it sounds like this will actually mess things up on the file system, which is not what I want (I have complete no-intro sets and I'd like to keep the files matching the datfiles).
Thanks!