When starting the local dev environment with version 1.9.x (and possibly earlier), you can pass this argument to dev_appserver.py to simply clear ALL of them, regardless of whether they have documents:
--clear_search_indexes [CLEAR_SEARCH_INDEXES]
It doesn't seem like there is a way to clear a separate index, although based on the statuses of the problems published above by Ani.
random_stackoverflow_user
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