I had to re-read the OP to see that the issue is being brought up because of the rising black level. first off, VLC doesn’t have color management and although prores, dnxhd/hr, cineform are all high quality, they are not lossless, they are very high bitrate 10/12 bit codecs.
There are some lossless codecs like png or animation but those are only 8 bit. Unless you’re uploading to youtube(which is 8bit), color grading requires 10 bit or higher at 444 chroma sampling. ffv1 or image sequences in color trillions is 16bit, but the sizes are excessively huge.
You need to weigh your final output destination, quality/generation loss against disk requirements/storage space. If you can import quicktime motion jpeg back in and the blacks look ok, then great! just ignore VLC’s playback(possible with Nvidia control panel 0-255 16-235.) and instead, install MPC listed below. besides quicktime player should never be used, (security problems/gamma tag issues)
video players:
https://mpc-hc.org/
can work with madVR https://madvr.com/
Calibration products supporting madVR: (sorted alphabetically)
· Argyll CMS
· CalMAN
· dispcalGUI
· HCFR
· LightSpace CMS