Hard to say like that ...
Scenario # 1: converting a single large PGN file
The tool is optimized for multitasking so you should split your large PGN file into several small PGN files.
Scenario # 2: converting multiple PGN files simultaneously
It will suffice to move the PGN+PLAIN files that are completed before restarting the process with the remaining PGN files.
There is a backdoor : create a file called override.ini and write the new ending date/time you want (by default the ending date/time is the starting date/time + 1 year). Then you have to move the PGN+PLAIN files that are completed.