Is your computer has win98 installed and you want to upgrade to win98se, then make sure you have all drivers *before* upgrading since the win98se install will ask you for drivers it cannot find in its own database.
After performing the upgrade, make sure your drivers are installed and working. Do not plug peripherals in your firewire while upgrading, this can confuse win98se install.
It is very safe to do this operation, but, as a rule of thumb, make sure you have a good bakup in place before upgrading...
Some makers like to tell customers that they need a fresh install on an OS just to make sure they driver will succesfully load, but in real life, if you are somehow proficient with a PC you can make it work without the reinstall.
Anyways, if after the upgrade to win98se your firewire drivers do not load, dont panic. Just do something simple: Boot in safe mode, run the uninstall procedure of your firewire drivers or devices, reboot normally and restart the firewire driver/device installation.
I have done that 100s of times with no problem.
BTW next time try to be a little more specific with brands and models of your devices. It will help us help you!
Bye,