This may or may not work for everyone but I have found that if I go into the Apple TV's Video and Audio settings and set Match Dynamics Range to Off, HDR comes back in the Prime App.
So if I set the ATV video format to 4K Dolby Vision, I get DV in the Prime stream; if I chose the format to be 4K HDR, then the Prime stream is in HDR. If I set the ATV video format to 4K SDR, then I get the Prime stream in SDR.
With Match Dynamics Range to On, no matter what the ATV video format is set at (DV, HDR), I will get a Prime stream in SDR.
Your mileage may vary and of course requires you to be watching viable HDR content of some type but I will obviously be leaving Match Dynamic Range off for now. Quite whether this is Apple or Amazon's issue to fix I don't know.