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The usual thing is last in first out unless you tell them otherwise in writing.

I believe that first in first out (FIFO) is the default. Also the broker or whoever must acknowledge to you in writing if another method of calculation is used for tax purposes.
But I agree that if you are diligent in setting up a spreadsheet and entering the data regularly the process is manageable. It also makes the process a bit easier if the entire lot is sold as a single transaction. In this way the short term transactions and long term transactions can each be summarized into a single entry on Schedule D. Since the Schedule D entries are based on total cost paid and total cost received and average cost for each will be the correct entry.
I would not depend on the broker or transfer agent to do what you should have been doing for the past 10 years when you sell.

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