@Jeff_Davids Briefcase has an experimental pull option in the settings that can drastically speed up pulls. I'd encourage you to use that setting. If you don't see in it settings, update to the latest version of Briefcase: ODK Briefcase v1.9.
I agree with @ggalmazor that this problem is either an issue with the data store or the API. I've looked at the data store and it looks fine to me, so it's very likely the API (or how we handle intermittent errors in the API).
I don't think you'll have to do anything as intensive as delete all the data and re-upload. The back up is just so we know the data is safe on multiple servers. I'm optimistic that this is an issue that can be fixed without touching the data. We'll know more as we keep troubleshooting...