The chunks get successfully destroyed, but new chunks do not have any ore!
Also, there are no biter nests being generated.
The trees come back though. But yes, please see if you can make the ore and biters regen. Somehow, the game does not think this is new land being uncovered.

Mine generated the bitters just fine. Cant remember if it generated ores, was just messing around with it

Can't repeat, every time have ores in the same place. http://imgur.com/a/Qz2qr

What mods are you use?

You need to regen the ores using the mod being affected. After regeneration is run once it'll keep placing the ores where they're supposed to go. PFR is /pfr_regen