I filed this enhancement request earlier today, if you also see this need as 
you experiment with indexes please star it:

http://code.google.com/p/googleappengine/issues/detail?id=5346

Building indexes for large data sets is expensive so deleting and recreating 
them from scratch needs to be avoided. With "NextGen queries" features the need 
arises to experiment with different index strategies for functionality and 
performance reasons. What I propose is a mechanism---probably through the admin 
interface---to disable an index for query purposes. The index must still be 
updated but is not used for queries until it is enabled again. When it is 
enabled the index is fully functional without any rebuilding overhead.

This way a user can put all the possible indexes in her index.yaml file, 
enable/disable some of them in production and perform tests/measurements. When 
satisfied she can vacuum the unnecessary ones.

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