…And should the free one be removed before upgrading to the paid version?
Welcome!
Please read the following two FAQ entries:
- MKVToolNix costs money in stores · Wiki · Moritz Bunkus / MKVToolNix · GitLab
- Launching the command line programs with the Microsoft Store variant · Wiki · Moritz Bunkus / MKVToolNix · GitLab
They answer your questions.