つ mkvtoolnix

Add the OP first, then append the content, then append ED.

Means you need to split the content first, then do the merging.
It involves more step, but you can do the split with mkvtoolnix too.

Softsubs, from what I tested here, it works fine (for both split and merge).

EDIT: There are some video editing tools that should allow you perform similar task too, but most of them are paid software. mkvtoolnix is my choice because it is open source and free.