If I understand correctly, your own created link for Findagrave is now gone and replaced by Ancestry's link to Findagrave.
I check one person in my tree that I know I had added a Findagrave link originally and it is still there along with Ancestry's Findagrave link. This is on the Burial event in the Profile page.
I just went in a changed my Findagrave source to include his name and birth date, and now both my source entry shows on those events as well as the Ancestry link for Findagrave.
Can you post a picture of what you are seeing that is different?
Edit: attached my example.