Sent in a request for assistance with the DE support team and received a reply back with a possible solution for others.
If you haven't done it already, try relinking your account on a different browser (maybe one you haven't used in a while). If this doesn't help, try clearing your cache/cookies and relinking the websites. It worked for me when originally the Warframe website was giving me the account error "could not find, try again later" and now is working properly.
Checked Warframe and received the rewards I was missing.
Hopefully this helps someone like it did me.