Starting with version 1.4.2, the Java SDK supports the vacuum_indexes action. Run this command to remove unused indexes:
./<appengine-java-sdk-path>/bin/appcfg.sh vacuum_indexes <myapp-path>/war
On Windows with the Eclipse SDK, this is something like:
<eclipse-path>\plugins\com.google.appengine.eclipse.sdkbundle_1.4.3.v201103311225\appengine-java-sdk-1.4.3\bin\appcfg.cmd vacuum_indexes <myapp-path>\war
source share