Since I do SDE administration, I've got about 2 dozen SDE connections, 8 ArcGIS Server in my ArcGIS Pro Favorites. Sometimes they disappear from the favorites list but not the favorites folder. In other words, they drop out of favorites.json. When I go to add one back in the new name ends in a (1). So I end up adding a duplicate to Favorites and click on the "Add to project" it will add both the original and the (1) to my project.
This has been occurring for well over a year in multiple versions of Pro. I tried deleting the duplicates and removed favorites.json but Pro doesn't know how to recreate it on its own so I restored the original. This acts more like a beta product than it does a professional software package that costs thousands a year. Sorry for the rant.