As with issue #4720, I am encountering the same issue with regular atlases:
this.scene.load.atlas("mykey", "/path.to/mykey.file"");
...loader says loaded and textures within atlas work. Later:
this.scene.textures.remove("mykey"]);
this.scene.load.atlas("mykey", "/path.to/mykey.file"");
...loader says loaded and textures within atlas do not work.
Perhaps the same fix should be applied here? The same code sample from #4720, but using a regular atlas reproduces the error.
Thanks!