If you got that error, its the first attempt at deleting the poll table. It doesn't do anything before that, so your old poll tables shouldn't have been touched.
But why would your old polls not work? But wait again, Gargoyle, you're upgrading from a version 2 of the poll mod. So you would already have the new poll tables. You didn't need to run the upgrade. ServerHacker is using version 2.0.2 of the polld mod. The upgrade is for anyone who uses the poll mod before v2.
It wouldn't be your files that would be the problem, but your database. So if you made a backup of your database, then you would be cool.
I did tell you (or at least gave you an idea) of what version SH was using. Although I do admit there is a small bug in the upgrade script (I just checked it)...BUT I still don't see how it should have affected your polls.