Thanks NOP

That would work but it's too slow, and I'm also thinking of a system I can set up once for other people.
So it's got to be a single button press to update everything.
I see 2 solutions at the moment:
1.
Command line ROMlister would work for me.
When I make them a new control panel, eg missile command. All I'd have to do is give them a new batch file which runs one additional ROMlister list creation. Oh, and add a new gamelist node to their MaLa tree.
2. A little program like this would work:
For every gamelist in folder C:\master_gamelists
Compare to the ROM names in C:\roms
and create (from the matches) new MaLa gamelists in C:\mala_working_gamelists
Then when I make them a new control panel, all I have to do is give them a new master gamelist for those controls. Oh, and add a new gamelist node to their MaLa tree.
I could probably work 2 out myself (given time), if it wasn't for the .mlg format.