I also have the same problem. After updating to the new ROM, none of the protected apps (free or paid) show up in the Market. I emailed HTC and this is what they said in response:
"I understand that you are unable to access some apps that you paid for after doing the update on your HTC Aria. The reason why this happens is because Google has an authentication process that they use when it comes to paid apps to make sure that you are using apps legitimately. When a new ROM is released for a phone, it usually takes a couple of days for them to update the database so that your phone is recognized. If it has been 2 or 3 days since you have updated your phone, I would recommend contacting the developers of the apps that you purchased. The point of this is that they can complain to Google and hopefully get them to correct the issues so your phone is able to access the apps you paid for and at the very least, you should be able to get a refund from the developer if the apps cannot be restored to your phone.
Sincerely,
Rafael"
Currently, other phones that just got firmware updates also have the same issue. Hopefully, this will escalate into a big enough problem that will force Google to do something about it.
"I understand that you are unable to access some apps that you paid for after doing the update on your HTC Aria. The reason why this happens is because Google has an authentication process that they use when it comes to paid apps to make sure that you are using apps legitimately. When a new ROM is released for a phone, it usually takes a couple of days for them to update the database so that your phone is recognized. If it has been 2 or 3 days since you have updated your phone, I would recommend contacting the developers of the apps that you purchased. The point of this is that they can complain to Google and hopefully get them to correct the issues so your phone is able to access the apps you paid for and at the very least, you should be able to get a refund from the developer if the apps cannot be restored to your phone.
Sincerely,
Rafael"
Currently, other phones that just got firmware updates also have the same issue. Hopefully, this will escalate into a big enough problem that will force Google to do something about it.