First, make a copy of your world, even though the stuff seems like it's gone now.
When that's done, I'd try manually readding the mod. There's a decent chance that the chests will be back. You could also try reverting the update and the loading the world in the older modpack version.
Usually Forge gives a message and makes a backup on world load if mod has been removed, so I'd double check your save folder for a backup as well.
Edit: You could also just cheat the stuff lost back in by opening to LAN and allowing cheats. This will also you to change game mode to creative, get the stuff back, change gamemode back to survival, relog, and then continue as normal.