I don't see a remux entry in log
that is an underpowered CPU
For me, remuxing only takes seconds (for a 7GB file) on a 8c/16t i7-10700K on a SSD... because the remux is only changing the outer wrapping, not the encoding. but that is on an SSD with plenty of free disk space.. I then have to delete the original MKV file.
You do have sufficient free space, right?