I upgraded from v11.20 SR9 on Win2008 (old vm server) to v12.10 SR3 on Win2012 (new vm server).
note: and a few weeks later did an in place upgrade to v12.10 SR4
We also upgraded our version of KliqPlan at the same time.
Because of the hardware and software changes, we decided to start fresh and not bring any of the old history / configuration to the new servers.
We did our initial validation testing by copying the apps over, running them and doing "blink" testing (web browser, two tabs, one for each server-app and control-tabbing between the two tabs). We did notice cosmetic differences between v11 & v12 (font sizes, object outlines, slight location differences) and some rounding differences (see the question I started on that issue - Qlik changed rounding in v12 to be what I would consider "correct") I did find a bug with ApplyMap() in v12 (search for applymap bug), but it is not likely to affect most people.