I believe the easiest, cleanest, and painless (for the innocent) way to deal with the "low cost" schematic debacle is to simply reverse the transactions from the market logs.
For everyone that purchased an affected schematic during the time when they were 1/100 of their normal price, simply subtract 99% of the normal price from their account. If the person still has that schematic, then they can sell it on the open market.
If they don't have the money in that account anymore due to money laundering, then it should be allowed to go negative so they can work off their greed.