create large number of 3D PDF files

I have about 50000 step files that I would like to convert into 3D PDF files. Is there any good way to do this? We moved about 2000 of them into a temp directory, then tried using Adobe 3D using Batch processing. First we tried selecting the files and found that there is a limit to the number of files that can be selected (we selected all of the files, however it gave an error that a file did not exist, and the error name displayed was part of a file name. It looks like the file selection dialog appends the file names into a string, and the maxium string length is too short for 2000 names). We also tried using a batch sequence which specified the directory. This ran for about an hour then died, with about 1/2 of the files converted. So based on these tests it looks like I will have to manually move the files into sub directories of about 500 files each, then batch process each directory (should be a fun couple of weeks). Has anyone else found a better way to do this?