I have such a bug only once. Then did not appear, although I did not admit errors when adding ores after that. I do not see much point in correcting this problem, it is absolutely not critical. Ores can be added manually through the config.
I would be more interested to see a plugin that will change the work of the cobblestone generator, for example, as in this plugin, but he must recognize the fluid from the mods. Maybe I’ll make this plug-in later, if I have a desire to write it myself.