One can still change Brother's Keeper's internal text files once many notes have been made BUT one needs to take certain precautions. Precautions many users may unknowingly neglect to invoke. I often capture out internal files to an external text file, re-arranged certain portions in light of newly discovered evidence, and then re-insert all the updated notes back into Brother's Keeper over the top of what was there before.
I don't know if preventing the type of error that happened to you should even be programmed into Brother's Keeper. I think it's more of an experience issue: just a slight bit of "thinking outside the box" on the part of the user. Something one necessarily learns by experiencing the often onerous consequences or from cautionary tales by others such as yourself.
Grit your teeth, rebuild what you lost, and chalk it up as a learning experience. I can assure you it will very likely never happen to you again. And maybe not to anyone reading this forum, either.