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assuming your calc 3 and diff eq classes is taken through a local community college or 4 year college, med schools will be see the courses (and the grades) since applicants are required to send official transcripts from every college where they have ever taken classes. Most med schools will allow those classes (if taken at a CC or 4 year college) to fulfill admission requirements for “college level mathematics”. However, be aware that some medical schools have specific math requirements. The most commonly required math class is statistics or biostatistics. AP stats usually will not fulfill this requirement.
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It will depend on the policies of your undergrad whether you will be allowed to retake the coursework and earn credit.
On AMCAS, you will need to mark any re-taken coursework (including any for AP classes for which you earned college credit) as a repeated class. This is non-ideal since both the original grade and the retake grade will be included in your GPA calculations. Re-taking classes you’ve already passed looks like grade grubbing/GPA fluffing/perfectionism/neuroticism–something med school adcomms really don’t like to see.