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As a matter of course, Adobe doesn't recommend manual deletion of the files in the Global Document Store (GDS).  As these are temporary documents, LiveCycle should be clearing out files in the GDS based on the settings in the Core Configurations (using adminui: Home > Settings > Core System > Core Configurations).

http://kb2.adobe.com/cps/807/cpsid_80778.html

LiveCycle won't tag files in the GDS for removal until they are no longer being used.  So if you are calling Generator as part of a long lived process, and that process has not terminiated (for example due to a stalled operation), then the files will not be removed.

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