When merging Donor Acknowledgement Letters, there is an option under Format to select how the letters will be sorted. Query is an option and the merge should be based on how the output is sorted in query.
We are currently evaluating this issue and will update this article when we have more information.
Steps to Duplicate
Create gift query
Add output fields
Choose field(s) to sort by
Save and close query
Go to Mail > Donor Acknowledgement Letters and create a new letter
Add query and create letter
On the format tab under Sort, select to sort by query