Having trouble multiplexing video segments together

Hey there,

Newbie here who could really use some help. Here’s the break down…

I ran a disc through MakeMKV which broke it into 11 .mov segments.

I ran 10 of those segments (I’m leaving out 1 of them) through Handbrake.

7 of the segments are 1024 x 768.

3 of the segments are 640 x 480.

I set handbrake to create mkv files, at video encoder H265 (x265), FPS: Same as source, Constant Quality: 23, and compress.

I planned on using MKVToolNix to start multiplexing them back into one file, but it isn’t working.

I understand that all the segments must share the same codecs (e.g., H.264/AVC or H.265/HEVC), resolution (e.g.,), frame rate, and generally the same audio track configuration.

Also, something of note: This is an old instructional dvd that was made using Flash Macromedia. I was told this could be causing some problems for me.

I have tried everything I can think of to get them the same, but I keep failing. Can anyone help me with what I’m doing wrong and how I might accomplish what I’m trying to do, please?