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 move 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?

Polling interval is 60 seconds.
Do I have full permission? What is the user ID that XI uses? The files are placed in the XI server so this should not be a problem, I think.
I also have "Process Read-only Files" turned on.
The files are coming from the same exact source so if this was the problem I would expect this to happen with every single file.
Yes, I'm doing CC, but nothing fancy, all the lines have the same structure and they are just moved to an identical XML structure.
In RWB I only see the "successful" messages for whatever actually got picked up, no errors.
This morning 2 of the 252 files got picked up. However at the same time 325 files of another interface did get picked up and succesfully processed.
I also changed this morning the file permissions on these 250 remaining files to rw-rw-rw- but still nothing happened (it used to be rw-rw-r--)
I'm still in the dark...
Thanks,
Viktor

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