You can run a batch of maps using the 'File→Run batch…' menu option. If you select an L3DT batch file (*.run), L3DT will make all the maps in the batch sequentially and auto-save each one. If instead you choose a map definition file (*.def.xml), L3DT will make one map using that definition and will not auto-save.
L3DT does not as yet include a nice easy way to generate batch files. This is on my to-do list. However, the RUN files are simple text files, so you shouldn't have any problem working them out. The syntax of the DEF.XML files is a little more complex, but these files are automatically generated for each project. Thus to make a DEF.XML for a batch run, simply generate one copy of the map in the normal, manual way.