No issues so far, beyond the occasional weird behaviour in multiplayer where different mods are installed on each end. Not relying on that though, one of the first mods I set up was BetterServerConfig which keeps dozens of layers of automated backups. Most mods have either worked as normal after updates or just been entirely disabled - I try to avoid things that add new items and entities or require server side installation.

Given that the vanilla game plus Steam cloud seems to have a regular habit of nuking people's progress anyway I figured there wasn't much risk to experimenting.