GetIncrementalUpdates method returns only records modified by users. System updates, like Email Delivery stats or email deployment updates are not showing up in the GetIncrementalUpdates results. 

For example email message is created on 1st day of the month and scheduled to be delivered on 15th. It has not been touched since 1st. Email delivery stats like SendStartDate, hard and soft bounces, open count, will be updated on 15th, then on 22nd, but to synchronize the record with GetIncrementalInserts/GetIncrementalUpdates methods, the synchronization window has to go back all the way to 1st day of the month. 

The same goes for Constituent records added by data sync. They don't show in GetIncrementalInserts until their predup status is cleared, which can last weeks after big data appends. We had 32,000 records added to the system on 5/31. They were not visible in GetIncrementalInserts until 6/13 and even then they are only showing up in the sync when synchronization window goes back all the way to 5/31. With varying period of time of before the records are eligible to show in GetIncrementalInserts it's impossible to know what synchronization windows to use to make sure all records are synced properly.