Using Files to control the conversion is good. I would not convert more than 100-150 per session, as you must determine if there were any errors and cif xthem is they occured, so limit the numbers of files acted upon at once. If you are performing the conversion with the server running, perform the task during off hours when the server is not too busy
You can also run two or three of the tasks at a time, if the server is not too busy