For arduino, adding a .h include is adding the library

If you would like to see the source of the library in the solution explorer,  click "vMicro>Show hidden files"

That meant you had "create shared library" enabled on the add library menu, and have subsequently switched it off. It is not recommended to use that without fully understanding how it works because it traps you into a specific library version.

It is better to use the "show hidden files" option. That shows the sources in the solution explorer but automatically switches them to be correct when switching boards or updating library versions.

To avoid confusion, I recommended removing any shared library projects from the solution. We are considering moving the "create shared library" setting to somewhere less obvious.