I can confirm: I updated a test 9.0 R2 box from SP2 to SP5, and the popup client files remained at 9.0.8959.259. I upgraded that test box to v9.1 and built a new package, and its file version was 9.1.9474.317.
I also confirmed that an existing client running v9.0.8959.259 was still able to print.
You can upgrade right from any Service Pack level of Uniprint 9.0 or R2 as well as previous versions of Uniprint. You just need to make sure that the version of OS and SQL are supported and all pre-reqs are met. For more detail, please see the Uniprint 9.1 Upgrade Guide in the documentation section of the Uniprint page.