Same issue here, developing on Windows, nearly all default settings, just 
upgraded to python 2.7 and SDK 1.8.9 from 1.7.2. Local datastore (sqlite) 
now empty. 

Tried to reload everything from scratch with appcfg upload_data, reports 
all entities successfully uploaded, but randomly missing about half the 
records. Frustrating!!!

Any solutions available?

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