You can write a few batch/script files that would:
1) run the foldtrajlite program with buffering on, so that you generate lots of structures without uploading them
2) upload all structures, then quit the program
All of the instructions and switches for doing this are in the ReadMe1st file.
When you are using your Internet connection, you would run batch file 1). When you are not using your machine, run batch file 2).