It's conceivable. It's pretty likely that if you opt to leave your vehicle alone (not having the "fix" done, whatever it might be), you get nuthin' (aside from the $1000 that you already got). But this will be your choice. It looks like it has been recognized that people aren't going to be willing to have their vehicles modified without being encouraged ($$$) to do so.
It remains to be seen what will happen to people who have crystallized a loss by selling the car. There are many different scenarios here. There are people who have already sold, and taken a loss. There are other people who want to keep the car but will not want the car modified no matter what. Others haven't sold yet but won't want to keep the car post-fix. Others will put up with the modification but only if there is some encouragement ($) and only if there is a good strong extended warranty to back it up (personally, that would be my choice - No way would I want a retrofitted SCR system if it weren't backed up by a LONG no-excuses warranty.)
I've said this before ... but if they want to retrofit SCR, as far as MY opinion is, the complete text of the emissions warranty has to be similar to "The cost to the customer of causing a "check engine" lamp to turn off shall be zero, and the cost to the customer of passing a state/provincial emission test shall be zero outside of the actual cost of having the test performed once." END. No mention of age, no mention of mileage, no more refusing to pay for a clogged EGR filter because the main DPF failed, no more replacing the DPF but not paying to replace the sensor that caused regens to fail. They make a Rube Goldberg emission control system ... they pay to keep it working. If they don't do that then the TDI in the family (my sister's) isn't getting fixed and my friend's almost-identical TDI isn't getting fixed.