Exporting/importing master pages: between separate projects, you import/export the master page sets. Once you’ve imported a set into a project, you can then either import individual pages from those imported sets into existing sets in the new project, or change the master page set used in layouts in the new project to the imported set.
E.g. by default your full score uses the “Default Full Score” master page set. If you import an “Imported Full Score” master page set, that set now exists in the project but until/unless you change the set used in the full score, it will still use its “Default Full Score” master page set.
You can change the set in use by opening the layout, then selecting another set from the “Current set” menu in the panel on the right.
If you’ve definitely done that, can I just check that the changes you made in the source project were to the master page, and not on an individual page as a page override? Can you share a zip file of the two projects perhaps?