Hey,
Hmmmm....I don't know. Again, you'll have to look on the PDF file. Whenever I update anything on my synths, it usually says to back everything up onto a computer first. In my case it's pretty simple because I'm only dealing with patches and programs, it's just sysex data bulk dumped into a sequencer. In your case, you have sequences and sample data as well...
Is your Triton hard drive partitioned so that the OS is on one partition and your files on another? If that's the case, you should be alright when updating because it should only effect the files on the partition where the OS resides, your data files should be left alone.
I've never played with a Triton seriously, so I'm advising you with the understanding that it behaves like a computer...please consult your documentation or even shoot Korg an email before proceeding if you're not certain, I'd hate to see you take my word as gold if I were wrong...
Take care,
Nick