What if you had the gps data as children of each entry and then used a 
keys-only query to match, and then fetch the parents. I forget the 
technique's name, maybe someone else remembers.  The benefit is that when 
you need to edit gps coords you leave the parent alone. Data in the parent 
isn't duplicated and all changes only happen to the children. No parent 
data is re-indexed so you reduce datastore charges on updates. I'm not 100% 
sure it'd help but it might be worth testing.

Also, I don't know the order in which you're going through your data, but 
there could be a hot tablet issue on indexes if you're changing lots of 
closely ordered data as you go. See 
http://ikaisays.com/2011/01/25/app-engine-datastore-tip-monotonically-increasing-values-are-bad/
 - 
not sure if it applies in this case, but it's possible you might get some 
weird side effects if things are being retried, etc.

Aside from that, if I were you I'd pay up for a premium account (at least 
for a few months, not sure if that can be done) if you don't have one 
already and the team isn't helping you offline. Hopefully they are!

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