When clean compiling, if there is no longer any resources used and the .rsc file is removed, it will still show in the File Tree until you close and re-open Dream Maker OR if you delete a different file from the list.
Expected: The rsc file to no longer be shown on the file-tree list immediately after being removed due to a clean-compile.
On version 354, it still shows the resource file after removing all connections to any resources and clean compiling, however the resource file still exists in 354 for some reason. It doesn't get removed until you hit the Update button on 354.
On 467 it is the same, unless you delete another file, close and reopen maker or hit refresh, (It's not that big of a deal to hit the button. so this could be one of those *eh* kinda things.)