Follow steps 1-7 above (excluding step 4) for each part (file) of the video

Re-encode with FFmpeg using timestamps and duration in the video denoted as hours:minutes:seconds.milliseconds (hh:mm:ss.ms), -ss is the start position of the encode, -t is the duration, make sure to use lossless codecs again to preserve the quality of video and audio

ffmpeg -ss hh:mm:ss:ms -accurate_seek -t hh:mm:ss:ms -i "title.cd1.mkv" -ss hh:mm:ss:ms -accurate_seek -t hh:mm:ss:ms -i "title.cd2.mkv" -filter_complex "[0:v:0][0:a:0][1:v:0][1:a:0]concat=n=2:v=1:a=1[outv][outa]" -map "[outv]" -map "[outa]" -acodec flac -vcodec ffv1 -level 1 -coder 1 -context 1 -g 1 "title.mkv"

Add chapters as described in step 9 for the resulting one file video

Re-encode with HandBrake using either the GUI or CLI version with a preset with Settings explained above, since the video is already cut to the correct start and length positions you don't need to specify those in HandBrake