Hello!
I've found when working with 3D models and the scene importer, this issue sometimes occurs as well.
The way I found to fix it is to re-import the 3D model again with the scene importer, and that almost always fixes the issue (though a couple times it took another re-import to fix)
I have a hunch that the font files work the same way, so maybe re-importing will fix it?
I'm making an assumption based on my own experience (I admit I know little of how the engine works under the hood :) ), but I think the issue has something to do with checking if the files have changed, since Godot automatically imports changed files. Somewhere it seems to store the absolute path, and it (for some strange reason) uses the files in the absolute path over the files in the project. I'm fairly certain it's a bug though, since I cannot see any reason why it would want to use the files in the absolute path instead of in the project. (though there could be a good reason, I'm just not personally aware of any :) )
One way to check if you've fixed the problem is to import the fonts, then rename the folder you imported from and see if it complains.
Hope this helps!