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Start with:

Sync your device with your WebDAV or MobileMe services (so your backup is up to date - this step takes some time if you have a large database and/or a lot of zip files).

When the sync is completed change the settings under Sync Settings to Nothing.

Go back from the Sync Setting and go down in the Settings screen and select Compact database. That would result in 2 zip files.

Then go back to Sync Settings and select your WebDAV or MobileMe services. Sync and you will get the question Keep local or server data select Local data.

After that you are in sync with a minimum of zip files.

I normally do this one time per day.

Good luck.