All of ffmpeg's de-interlace filters have the option to de-interlace frames that marked as interlaced and leave the others alone.

https://ffmpeg.org/ffmpeg-filters.html#nnedi

Set which frames to deinterlace, by default it is all. Can be all or interlaced.

It would be great if NVEncC's interlace options had the option for the same. Right now on hybrid content it will attempt to de-interlace progressive frames giving it a "shimmering" effect.