Since originally posting this I have spun up a staging site and run it using 2014 theme and only EDD and Modern Tribe plugins activated and I’m still experiencing the same issue.
Sorry to hear about the troubles. I just did a quick test on my local environment but was unable to reproduce the issue described. Is this happening with one specific event or multiple events? Can you send over a screenshot of a ‘Download’ you’ve set up that is giving you the problematic link in the emails? (see screenshot below)
Thank you for reaching out and I look forward to resolving the issue with you. Have a good Thursday.