Can you modify the script and do a Partial Reload? If you add the following to your script:
REPLACE DROP TABLE BigTable;
Make sure that is the only command with the REPLACE prefix. Then do a Partial Reload. On a Partial Reload, only commands with the REPLACE prefix will run. I did some testing on the app I'm working on and it seemed to work fine. I would make a duplicate copy of the file before you try it, just in case.
Another option is Reduce Data, but I don't know if it would be possible to get rid of just one table using that method.