I am using a nexus mod which needs its plugins listed in plugins.txt

But for some reason, starting the launcher empties this out.

Is there some way to preserve the file (other than repopulating it every time, which works, but is a minor annoyance)?

My Fallout 4 folder containing the plugins.txt file is set to read only. I was wondering why I never had problems with the plugins file because I never set it to read only. Maybe some app set my Fallout 4 folder to read only. Anyways try setting yours to read only.