I am also getting some confusing results with ProRes output though I’m not using ProRes input.
Davinci Resolve and Premiere Pro both report different frame counts than the original. However, when I load the output ProRes file back into VEAI it reports the correct frame count.
I’m upscaling some hybrid DVDs and using Avisynth IVTC to deinterlace, extract variable frame rate time code, and load directly into VEAI. After upscaling I am use Resolve to correct the aspect ratio and do a slight color correction before exporting them for remuxing with the audio and the new timecode. However, since the frame counts don’t match the original, anything muxed from the ProRes files doesn’t sync with the audio.
I too am trying to preserve as much detail as I can before the last h.265 compression.
The only way I’ve been able to ensure the correct frame count is to export to PNG which isn’t the end of the world but much more difficult if I need to move the files, not to mention the time it takes just to delete all those files.