I’ve been able to create a flight plan in MSFS with one or more custom waypoints. Each flight plan reloads successfully from the World Map each time even when using different aircraft. I’m loading a saved flight plan directly, not using any FLT files.
I don’t think you said which aircraft you are using. I’ve been using stock aircraft with no add-ons. Unless there is a difference in aircraft, I don’t have any explanation why you are having a problem.