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Join nowHi there, @Montgomery Minds.
Yes, you're correct, there's no way to fill in the estimate amount by hand when deleting the item on the estimate. On the other hand, yes, the reporting would be inaccurate since the estimate items are deleted.
What you can do is, remove the check-mark on the Billable column when tracking customer/job so the amount won't add to the invoice created.
For more information, you may check on the article provided by my colleague MaryLurleenM for additional information about tracking job costs.
Feel free to add a post if you have any other questions about estimates and invoices. I'll be happy to help you!