That's the beauty of it. Just be sure to keep your "last good" 6324000.IMG and TDB some place so if your compile goes wrong, you won't have to re-install MapSource. If one of those is bad, MapSource will say the installation is bad and to re-install. Really all you have to do is replace the bad TDB or IMG.
This is the place to look for mkgmap. I've tried r1404 and haven't had any problems yet except one specific to a complicated topo I'm working on in MP format. I doubt it should give you any problems at all in making up your TDB and IMG files.
One other thing:
The xmx parameter in the batch file sets the amount of memory Java will have available. (1280 is the maximum Java can use under 32 bit Windows.) The actual memory available will be affected by the amount of memory available after Windows is loaded. If mkgmap quits early, or doesn't run, try making that number smaller until it runs.