I think there's no problem at all.
I read in an other place (spanish site
http://www.todopocketpc.com) that there's no way to restore from the backup done with ActiveSync, but this pot was related to a ROM update of the Toshiba.
That's way I make a backup of my PIM data with the Data Backup utility of the Axim.
Let's put everything straight:
1. Make several backups:
1.1 PIM data backup, or even all data backup with Backup Data utility of the Axim (make both of them),
1.2 Make a backup with ActiveSync (even it didin't worked for me),
1.3 Finally, make a sync of all of your data with Outlook (just to have all of you contacts, appoinmets, e-mails, etc)
1.4 ... and if you have your own utility.... give it a try also!!!
2. Copy all of your files to your PC, even the built-in data. if you have a CF card.... put them there also.
3. Make the ROM update.
4. Try to restore any of the previous backups. The one that worked for my was: PIM data with Axim Backup utility, and move back the filkes from my PC to my Axim. (I don't have a CF card

)