Removing a layout using the designer fails if the app is not compiled.
Steps:
1- Create a layout using the designer.
2- Compile and execute.
3- Go back to the designer and delete the layout.
4- Exit B4A.
5- Re-open B4A, it will complain that it cannot find the already properly deleted layout.
Similar case when renaming or deleting modules, if the app is not compiled, the IDE doesn't refresh the list.
It is not really related to compiling. It is related to saving (which happens when you compile your app). You need to save the project after you remove the layout as the layout file was already deleted.