Where's the project located?
While I'm sure you are sorry you upgraded, I can attest there are many that have no issues with upgrading. I'm one of them. I guess I'm just fortunate.
Did you encounter any messages that hinted at errors during the process?
Depending on what's going on, sometimes RoboHelp can lose track of one or more files. It's not that they are actually deleted, but for some reason the tracking gets messed up. That's what Jeff was hinting at when he asked where your project is located. One of the known issues for this happening is that your project is actually on a network drive. And when that is the case, because of something called "latency" (meaning a delay) RoboHelp can lose track of things and corruption creeps in.
Helpful and Handy Links
I'm coming at it from a different position than Jeff and Rick.
RoboHelp 8 had a problem where topics were lost from Project Manager. It was fixed with the 802 patch.
Did you have that patch applied? If not, it maybe that RoboHelp 9 revealed what would have happened anyway.
I know it doesn't make much sense that your colleague could update and you couldn't but worth a thought if this is not a network project problem.
See www.grainge.org for RoboHelp and Authoring tips
The file is located on my c drive in the Robohelp project file.
Version 8 had the patch applied.
The error message that I got when trying to upgrade the files from 8 to 9 (from within 9) looked like a memory error.
The instruction at blah blah referenced memory at blah blah. The memory could not be read. Click ok to terminate the program.