I was rendering this video when I tried to do something else on my computer, and that could always cause the video to render some black frames in the video.
It only happens with MC 1.16+replay 2.6.0/1, while 2.5.2 could render a full video with no missing frame(also the same environment).
This is the launching log and ffmpeg exporting log:
latest.log

export.log

That's the Dynamic FPS mod working as intended.
I'd recommend you open an issue on their tracker and suggest they implement grondag/frex#9. Until they do, you'll have to manually disable the mod when rendering or keep the window in focus at all times.