Yep, sorry about that. Spine makes a backup in <user>/Spine/backup/hotkeys.txt before changing it. When new hotkeys are available, Spine rewrites the file to contain the new hotkeys, preserving your existing hotkeys. Sometimes the hotkeys need to be replaced though, eg when old hotkeys have been renamed. In that case you'll have to redo your hotkeys file. This should be rare.
In 1.7.00 the preferences had to be reset to change some defaults. This caused the hotkeys to also be reset.