How to losslessly replace a specific area in a range of frames
I don't know if FFmpeg supports the Camstudio Lossless Codec, but if it would. Then replacing the area with a PNG file (hence: adding a logo) could be a solution.
The explanation is done here at &quot;Timing the overlay&quot;.
https://superuser.com/questions/683643/how-to-add-my-logo-for-the-first-30-seconds-in-a-video-with-ffmpeg
In that example codec:a copy was already given (for audio). If you would take any lossless videocodec the result will be lossless.