.meta not being read
I just imported a project that I had been working on on a Mac last year onto my Windows from github. Because I had 2020 Unity on my Windows, but the Unity I was using on Mac was a 2019 version, so Unity Hub prompted me to install that version. It also asked me to switch to some kind of Windows dependency from a Mac dependency (I don't remember exactly what it was.) I finally opened the project and something is off. The white icons on the screenshot should all have # on them instead for C# because they are C# files. When I opened it up, Unity immediately gave me an error saying that type or namespace name Waypoints could not be found, so I removed the Waypoints.cs.meta file from the folder to see if it would make the error go away, and it did. Hence the # icon for Waypoints in the Assets pane. It seems that there is some dependency that is not being updated. Any ideas?
When things like that happen, it's usually a thing with importing. Maybe selecting Assets>Reimport All could fix it? If it doesn't, maybe you could try deleting the Library folder in your project, I'd suggest doing it with Unity closed.
I think deleting the .meta file worked because it forces a reimport of the asset, but it is not a great solution, because you may loose a lot of references to scripts in your project.