Thank You!, Will RIP I think downloading it again without merged chapters is better than encoding all the episodes
You can use MKVToolNix GUI v24.0.0
1. Under multiplexer tab, just drag the OP file first or add the file using the menus.
2. Drag/add the main episode file.
2a. A window should pop open asking 5 options, make sure to have "append to an existing source file" selected.
3. append the closing(ED) file the same way as step 2.
4. Just in case, under Output tab, I would change the File title to whatever you want.
The original name of the OP file title is the default otherwise.
5. Click "Start multiplexing"
Let me know if this works!