But what about schools that "delete" the first grade if you retake a class? I know it's technically not on the transcript anymore but it was at one point, right? I feel like it's best to be honest. It's really hard to say. I think the Registrar's Office sends student transcripts at the end of every semester to the National Student Clearinghouse so in the case of a deleted grade, it may be possible they have records of the original grade even if your institution doesn't list it on the official transcript.
This is really all speculation but I feel like the best thing to do is be honest as AMCAS expects you to report every grade you've ever received even if your school has internally deleted it. I read somewhere you can order a transcript from the NSC so you should try to order one from there and double check with that before inputting grades in AMCAS.