I have had some problems upgrading both Repetier Server and Repetier Firmware. This is regarding Repetier Server 0.86.
The machine is a D-Bot (CORE-XY) derivative with 3 Z motors and a BL-Touch probe, electronics are Due and RADDS, and a Raspberry Pi for Server. The bed is not very flat. but I have had very good results using Repetier-Server 0.80 and Repetier-Firmware 0.96 for over a year (thank you!).
I replaced Server version 0.80 with the latest 0.86 using the armel package, leaving the existing printer config and G-code files alone. To my surprise, the new Server seemed to be re-loading (or something) the existing G-code files. It was very slow, but the problem I noticed was that it changed the time estimates to be extremely large. For example, 187 hours rather than 6 hours (about).
I ended up using a new image instead due to other problems, so I can't say whether this affected printing, but it was odd. Using the 0.86 image for the Pi, the times look OK.