This made me remember old set of tools called mtx2midi and midi2mtx, I used them to edit some midi files while making sure I'm not introducing any unwanted changes. While roundtrip output was not binary identical, it still sounded the same.

Looks like MTXT tool here does not quite work for this use case, the result of the roundtrip of a midi I tried has a segment folded over, making two separate segments play at the same time while the total duration got shorter.

https://files.catbox.moe/5q44q0.zip (buggy output starts at 42 seconds)