Hello theller85,
It sounds like you have started with a new SP9 instance and imported all of your solutions from your SP5 database, this works pretty well except for you cannot retain any attached files, I ran into the same problem with the new SP9 database not recognizing attached files also, I was not able to find a way to get the files loaded into the new SP9.
How we did the migration was by selecting to use the SP5 database when we installed SP9, yes this did bad tings to the GUI so if you tried to open the new SP9 version after the install, I don't think you could even see anything.
I went through and exported all of the com.aras.innovator package files from the SP5 installation along with my custom solutions before upgrading (make sure you back up the SP5 database, you will have to restore a few times) and spent a few weeks testing re-importing these package files back into the new SP9 database until I got clean imports, following up on all import errors to figure out what failed was a bit frustrating at times.
I'm guessing it's possible that I have somethings that are not connected properly in the new SP9 database but I have a stable SP9 installation that has been performing flawlessly for pretty close to a year. I will add that the more customizations you have the more difficult it will be to hunt down the import errors but Aras seems to be very forgiving when it comes to allowing little configuration errors.
I'm sure this is not the best news for your situation, but I am sold on Aras and was willing to make something work to keep the software alive, I'm sure if I was on the subscription service they would have a cleaner solution, but I did learn a lot about the Aras software through this process and I was quoted at $80K+ for a "migration" from an Aras VAR, so I think we did very well considering.
I hope this helps,
Bryan
