You don't lose anything except the security holes fixed in more recent versions
Use the upgrade version of the zip file and you'll have no problems. There are many features added since 6.04 as well, I think you'll really like it
It should also cure the problem you are having here.
Here's the guide to upgrading, ask in our install forum if you still have questions.
http://www.infopop.com/support/ubbclassic/UBB6_upgrade_within_6.html