The messages.json is a bit odd. I’ve noticed (at least before the update, but I assume it’s still the same), that the commit/version times are based on EST. I normally add a couple hours to the current time, then offset it to EST. It may be worth giving it a shot, since, as you said, may users will ask you why x,y, and z are not working anymore. In the worst case scenario, no one gets your message and you get all the issue creation you expect. In the best case, it works and people will (hopefully) read about the updates on the README. Setting up the messages themselves is pretty straight forward. I’m sure you have looked through the same documentation I have on wbond’s site.
Anyways, that’s my insight into the messages system of package control. I think it’s worth giving it a shot since, even though I’m sure you will answer the “why isn’t this working anymore questions”, you would be happier if you didn’t have to, or at least had fewer. Anyways, thanks for all the hard work (on this and your other plugins)!