The one in the scripts folder is the script for that file, while the one in the Resources folder is a scriptableobject. Because you updated from an old project, it might be possible that the old file either got duplicated or the metadata got assigned to the wrong object... The file used to be formatted differently in older versions of STM, so it's possible for something like that to happen... Does the error persist if you go into the text data editor (click the [T] in the top-right of any STM inspector), scroll down, and click "Refresh Database"?
When you search your entire project folder for "SuperTextMeshData", is the ScriptableObject and the .cs file the only two files that show up? If there's more than that, see if there's a copy of the ScriptableObject somewhere, that would cause this problem, too