Glad you got it working. Since you're backing up the file manually, you can probably run sce-remove SCE to remove the extension that didn't work for you. You'll have to reboot and see, however, as Flash does require some dependencies to function, which may still have been brought in by your *broken* flash SCE extension.
The size of your backup file will be a lot larger backing up the Flash *.so file, if this is an issue an alternative is to place the *.so file in another mounted partition and just sym link it to usr/lib/mozilla/plugins/. Then you just need to backup the sym link. Or if you are running dCore with a persistent /home/tc directory that does not require an exittc backup, then you can create a plugins directory in /home/tc/.mozilla/... directory and run Flash from there.
If you installed Flash v11, you'll need to manually download security updates from Adobe archives everytime Firefox indicates the plugin is outdated.