It is always a good idea to back everything up when messing with any files or changing anything; especially if things go wonky, you don't lose everything. I have not tried going from an earlier version to a new version, but I am 90% sure updating will clear everything out.
My personal preference is to clear everything out when a new Rom.
1. Wipe data/factory reset
2. Wipe cache partition
3. Wipe Dalvik Cache
4. Flash the Rom and reboot
Otherwise there is always a chance that something will get left over or not replaced from the previous Rom and can cause issues with the new Rom.