It's invested domestically in real estate, art, gold, or other assets, or held offshore, either in the form of freely convertible currency or other assets, which is why 98.96% of the cash was returned.
I strongly doubt a significant number of criminals openly advertised their possession of black money by returning it themselves.
Modi's ploy was an unmitigated failure.
For such a disruptive event, that's pathetic.
The only winner was the banking system, who saw one of their major competitors (cash), hobbled. Modi now seems to be saying that this was the point all along.
AKA, If you started with X money hidden then you don't get to keep 100% of that money if you hand it to other people to deposit.
On top of that people where caught, so actual black money disappearing was much greater than 1%.
There was a huge collateral cost, I don't think anyone can deny that, but whether it was worth is still too early to call.