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Buy nowHello, Chris.
I have one more solution to help you ensure you'll be able to import all of your budget data in QuickBooks.
If you haven't already done it yet, you'll want to check your fields that might've caused the missing and incorrect budget data.
An overview and a guide for header placements can be found here: IIF Overview: import kit, sample files, and headers.
You can also use the solution given by ladae007 and import the data in batches.
However if you still can't get the correct data and there are missing months, I would recommend contacting our support. They can look deeper into the system and check what's causing the issue:
Aside from using the Budgets feature, you can check this article for a guide if you need to utilize the Reporting feature in QuickBooks: Understand reports.
I'm willing to lend a hand again if you have other questions regarding the Budgets feature. If you have any other concerns regarding QuickBooks Desktop, please let me know.