It depends on the upgrade, if the firmware was on something starting with 071 then it would need to have a tech upgrade it to anything that begins with 072. Specifically this would be called a "Forced Altboot no data backup, no clone"
This does a clean install and wipes absolutely all data from the device. So total setup would need to be redone when the tech goes. The only 2 things that could be backed up and restored without breaking things would be the Address book and the user accounts for Xerox Standard Accounting.
Now if it was on an 072 firmware and just had a regular update, then it should not have caused any scan issues, the only applicable setting that should cause your outcome is in the template as seen here.
*If* that option is set to single page, it will create (in your case) 10 individual pdf files, and in that case it will create a folder to put those scans in. And if that is the case it is entirely possible that the user account doing the scan has the ability to see into the share folder and put a file there, but not to create an additional folder and put a file in that.
That is going out on a limb admittedly, but it is the only 2 possibilities I can think of. And it is logically sound I think.