While there are some anomalies that can creep into the stats based on how they are calculated, your brains should be the same.
When you sync your Brain, the differences between the online version and the local version are exchanged. These differences are calculated based on the last known time they were in sync.
If at some point this last known time is wrong, it is possible that some true differences may be missed. To attempt to correct this, you can try to use the "Force re-sync" option and enter a date that is far back enough to get the true point in time at which the brains were the same. You must do this on both machine once. After both have completed this once, do a regular sync from both machines. If after doing this, there are still differences, then that indicates that the date you set was not early enough.
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