Updating Cwicly

I’m worried about this in your changelogs:
" Please make sure to backup your current installation and to regenerate your HTML & CSS once updated"
I manage hundreds of multisite subsites, and just thinking of a scenario where I have to go site by site, regenerating HTML, gives me the shivers.

How is updating handled in Multisite? How is the backwards compatibility in (future) releases handled? I’d rather avoid converting sites block by block to a new version.