I upgraded a VM from 15.10 to 16.04 over the weekend
It trashed by XFCE desktop settings - no apps in launcher, none of the custom icons I'd set up, not even the wallpaper I'd used. The same command line "do-release-upgrade" from 15.04 to 15.10 on the same machine worked fine last time round. That's why I do this in VM's - I'd suggest waiting for the dust to settle a while, or do it on something not critical.