Using RTC (version 4.0.1) Plain Java API's  , the code to remove the build definition from the supported build definition list of the build engines as shown below is not working as expected i.e. build definition is not getting removed from the supported list of build definitions for the build engine.

Code to remove the build definition:
buildEngine_WorkingCopy.getSupportedBuildDefinitions().remove(buildDefinition);
ClientFactory.getTeamBuildClient(repo).save(buildEngine_WorkingCopy, new NullProgressMonitor());

But the add method to add the build definition to the supported build definition list is working fine as shown below:

Code to add the build definition:

buildEngine_WorkingCopy.getSupportedBuildDefinitions().add(buildDefinition);
ClientFactory.getTeamBuildClient(repo).save(buildEngine_WorkingCopy, new NullProgressMonitor());