You can't be made to love anyone. But there's a difference between how you feel about a person and how you treat them.
Both girls are now your granddaughters, so as a grandparent, you're supposed to treat them equally. Since this situation is new to you, it may take some conscious effort. Make sure you give the girls gifts of equal value (both monetary and emotionally) and at the same occasions. When calling them, speak to both of them separately. Ask both how they're doing, how their day was and so on.
Show both equal love, give both equal love.
Try to not emphasize your "extremely close bond" or that "beautiful relationship" too much. Words like "favorite" should disappear from your vocabulary, even in private conversation with either of your granddaughters. Neither of them must be made to feel more or less special than the other.
But some damage has been done. Your granddaughter overheard you on the phone with her sister, calling her your favourite. Her father was right to bring this to your attention.
Of course, you were used to calling her that. I assume (I hope) your son's daughter from his previous marriage was your only grandchild until he met his current wife. If you have other grandchildren, you shouldn't be calling one of them your favourite, regardless of the present change.
So it's now up to you to undo that damage. Talk to the girl youyou've hurt and explain that you were used to calling her sister that, but that of course you're very glad you now have two granddaughters and that you love her very much.
Try to spend some time with your new granddaughter alone, trying to get to know her better. You've had 4 years already for this, but better late than never. This is of course not easy when they live in another state, but plan some activities with each of them alone when they're visiting or when you're visiting them.