Hi there, whaley.
I'm glad you've reached out to us. Allow me to help and ensure that your custom estimate will import to QBO successfully.
We haven't received any similar about this issue. After you import your custom estimate template in QBO, make sure to map marked areas in your document to QuickBooks data file correctly.
For the detailed steps, you can check this article and scroll-down to Step 4: https://quickbooks.intuit.com/community/Income-and-expenses/How-to-import-custom-invoices/m-p/186467.
If the same thing happens, I encourage you to contact our QuickBooks Online Support Team. They have additional tools to pull up your account and investigate this further.
Please let us know how it goes by clicking the Reply button below. Have a good one.