Use NVEncC encoding externally:
Encode your video with NVEncC using a separate tool like Nvidia NVENC SDK or Handbrake (with NVENC encoder selected).
SVP can then process the encoded video without the HDR metadata issue.
Consider alternative hardware encoding options:
If you have a recent Intel Quick Sync Video (QSV) capable CPU, SVP can leverage QSV encoding which might handle HDR metadata better.