Base minecraft does not have anything other than a blocks hardness to determine how breakable a block is. And even then the apis used for directly editing the world assume that breakability has already been checked so any mod (or vanilla code) can, accidentally or on purpose, remove blocks from the world that should not be removed.
For the longest time even vanilla tree growth could replace blocks regardless of hardness with tree leaves.
As such, rotary craft mining bores, quarries from a variety of mods, custom explosives, meteor strikes / tornadoes and other such mod features all have the potential to accidentally bypass the block protection features of other mods.
The only thing to do is report any such found instances as bugs against both mods, in the hopes that they can come to some sort of understanding on how to honor each others mechanics. Reporting it as a modpack bug is possibly also good as the FTB team responsible for the pack should care to ensure the pack is "integrated"
