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In addition to the mental math confusion the other ninja mentioned ("Five plus six does not equal ten. Your app is buggy."), there's another advantage of the current behavior. It exposes more information about state changes in your database.

With a merged count, if a flagged item in your database became due soon, the merged badge count wouldn't give you any indication that happened.
The current behavior does expose that information. When you see that the badge has changed from X to X+1, you know that something's changed in your database.

(For similar reasons, I have my badges to count flagged and overdue, but not due soon. I wish there was a way to better differentiate between due soon and overdue in the badge, but we can't control the badge color, and we can only feed it a single number to display.)