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I'd expect NS to flag duplicates for you correctly in the second scenario - but now with the exclude functionality that is part of 2020.1 I wouldn't lose sleep over it if it didn't flag them appropriately

Second scenario, yes.  I was hoping that NS would flag the duplicates or otherwise exclude them from future matching to save me the trouble of having to remember which date I downloaded transactions through last. Thank you!!

If you downloaded them in different formats you might have trouble

i.e. if you did one as BAI2, and another as just a standard quicken file they might not flag automatically- but with the exclude functionality in 2020.1 you can just mark them as duplicates and move on

Good to know!  I've been utilizing the same format for all of my bank/cc downloads (qfx) just for consistency's sake.