When I try to launch multiple supervisors, overwriting cluster conf causes many exceptions as following:
"RemoteTrace: \njava.io.IOException: Resource hdfs://server-1597.novalocal:8020/user/hduser/.storm/appattempt_1372228184151_0003_000001/conf changed on src filesystem (expected 1372228657556, was 1372228657910\n\tat ....."

It looks like that overwriting causes the size of conf file to change and yarn throws exception due to the inconsistency.

In worst case, since containers can not be successfully launched and the setting of supervisor numbers can not be satisfied, the system will be in the loop of asking containers.

By checking the paths before overwriting avoids those exceptions as I experimented. Since the path will contain applicationId, reading wrong config from other cluster seems to be not happened?