It does not matter what you use if subproject or root project from IDE (e.g. last Netbeans). And if I remember right it is OK also with version 5.3, but issue starts occurring since 5.4. That means to me that you have to change proper file existence-checking or you have simply delete more then before and both things are wrong especially if I take to account that build directory is deleted at the end so then I think that you have just report warning instead of error and stop cleaning of rest of subprojects.
In any case I hope that you even test that from some IDEs before any release, because no all people would like to build gradle only from command line and develop in plain text editor.