The letters may be quite different if the projects are different. That will often be the case when you are looking for a job. You have just one cv that everyone sees, but the cover letter is particular to the job you are applying for. It's not immoral to say to two different potential employers "this is the job of my dreams because ...".
At the interview you'll have a chance to talk about all the projects, but each cover letter should discuss just one you are applying for.
Bring to the interview
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