Hi beltechs,
The Estimate number on the default estimates screen is actually just the RefNumber from the estimates table. This number is not required to be unique in Method or QuickBooks and even if you assign it a value that already exists in QuickBooks, you will not receive any errors. It is still best practice to allow QuickBooks to assign these anyway since things can get messy when you have multiple estimates with the same RefNumber. The transaction number (TxnNumber) is required to be unique and you will get an error if you assign a number which already exists in QuickBooks. I do not believe any of the default screens will allow you to assign this manually however.
When QuickBooks assigns these numbers, it assigns them based on the last number in sequence. If your greatest value for Invoice number was 5, the next one will be assigned 6. If it was 461, the next number will be 462. It does not matter if there are any unused numbers in between, the next number will always be one greater than the current greatest value. If you disable custom transaction numbers, QuickBooks will handle the sequence this way. Any estimates that are in error will need to have a unique transaction number assigned to them to fix this error.
If this does not solve the issue, please take a screenshot of your "Resolve Conflicts" screen. There should be more data there which can help me to resolve the conflict.
-Audisho