That was just my reply to Sune..... If you don't disable sets then fix-missing will most likely find roms inside your small collection which are also used for other sets (since it's pretty common that e.g. eeproms are shared through dozens of sets) which are not part of your collection. So it's up to you what you prefer: if you don't disable sets, you can remove incomplete sets later on or if you disable sets you yourself have to care about which sets you enable and which not...