I don't believe it's possible to install software directly to your PDA; you must have done this via your desk top machine. But that isn't really your question. One of the best sources of advice I've found for the Axim is
www.aximsite.com
If you can't get help there, I don't know where else you can. It's a very comprehensive site. Don't you have your software installed on your SD card? That's the safest place to put it. If so, it's in no danger. If in doubt, remove the SD card before you do the update. The Axim was also the first PDA to feature a nonvolatile memory which eliminated most concerns about lost data; don't know if this applies in your situation.
Sorry I can't be of more help.