I was a little surprised to see Microsoft announce Display Duplicate G/L Accounts on Budget Exception Report as a separate feature of the day as it looks to be part of the Budget Import Exception Report which is a new feature in Dynamics GP 2016 R1 itself:
The original feature of showing accounts the budget which don’t exist in Dynamics GP is going to be fabulously well received; this one is a very good addition which I think may not be fully understood by some.
I have had to explain to a few clients that having the same account on the file more than once will result in only the final value ending up in Dynamics GP as it will overwrite the previous entries. If you want to load values in multiple times and have the cumulative values, you need to load multiple budgets and then use the Consolidate Budgets feature.