Yes I think so...
Well you still have 2 options.
If both partitions are of a similar size, then you could just use WBFS manager (one that supports HDD to HDD copy/clone) to
1. Format your other (2nd) partition to WBFS
2. Copy over the games from 1st WBFS partition to 2nd WBFS partition
3. Format first partition to FAT32.
OR, if that's not feasible, if you have enough space on another HDD, use WBFS manager to backup all your games from the WBFS hard-drive, format it how you like and then readd them.
If you used the USB loader to backup games on the wii side, you will notice that it is much faster transferring the iso dumps from your PC.
I think, it could be faster than redoing it all from scratch....
MrTea: I don't know if there is any applications that can resize wbfs partitions.......