Old editor versions (< 4.0) all read the same hotkeys file: ~/Spine/hotkeys.txt. When you run a newer version, it adds any newer hotkeys. If you then run an older version, it doesn't recognize hotkeys that did not exist back then. It shows the error you see because it doesn't know if the unrecognized hotkeys are from a newer version or are hotkeys that have been mistyped. The error can be ignored.
Newer editor versions (>= 4.0) read a different hotkeys file: ~/Spine/settings/hotkeys-x.txt where x may be 1, 2, 3, etc. This means there is no errors when going back to < 4.0 versions. We will bump the x number whenever we need to change hotkeys in an incompatible way, instead of reseting all your hotkeys like older versions. There can still be the issue of unrecognized hotkeys when moving from a newer v4+ version to an older but >= 4.0 version.
