So you will just have to wait and see. I can recall other bugs of a similar scale that we just had to play through, sometimes there just isn't the info to fix it. For example I'm not sure the game would record how much gold everyone had before the tax for it to be restored, so in that case what should Tom do, just award everyone an average?
I took note of how many negative bonds there were before I wiped them out; if Nosferatus finds that the money does, indeed, reappear in the next tax, I know exactly how much to reduce it by to ensure that they don't get double gold.