You can do a couple of things here. I'd start by asking then to check their spam folder (or promo folder, if they're on Gmail) and see if they see the confirmation email.
If they do, problem solved! They can just confirm and start receiving your PDf and newsletters.
If they don't see it, you can ask them if it is OK to manually subscribe them. If so, you can just confirm their subscription on your end, and again, problem solved. Once you confirm them on ConvertKit and add then to a sequence (or tag them, depending on how you have your automation set up), things will work out the way they were initially set up to work.