The submitfile is generated by Pegasus. We asked the Pegasus people, whether directories can be used instead of a file list which is not trivial. Also changing the pipeline to reduce the list length is difficult. Would there be a way to make the submit more resilient to larger arguments?
If you have no other options, you can try setting TIMEOUT_MULTIPLER=100in your condor_config file, and restarting everything. I can't guarantee that this will work, and an 8 megabyte classad working its way through the system is like a snake eating a pig, but it is the best we have.
-greg