Hello there,
I am confused about what to do with the cards tagged as duplicates. I have already studied a lot of them and do not wish to lose that progress.
Hello,
I would be happy to help. 
It’s hard to say, as there may not be a neat solution one way or the other unfortunately. You could delete the duplicates, of course, though you will necessarily lose any review progress for those cards you choose to delete.
Or, alternately, you could choose to keep the duplicates in which case, well, you have some duplicates (which may or may not be much of an issue, depending on how many and/or how much it bothers you to have them)
Alternately, you can suspend rather than delete the duplicates if that works better to your liking.
Please let me know if that answers your question, and if there’s anything else I can help with.