I also ran into this issue. Mine was a fairly specific case but figured I should post a reply just incase someone else runs into the same thing.
I was using Hockey, now App Center, for testing. With my last build I was unable to upgrade in place. When I would attempt to install from App Center I would see the "{AppName} is already installed. To install {app}, delete {app} from your device and try again." After trying a number of things to fix this I was never able to get it working. I instead put my app on TestFlight where I was able to upgrade in place. We ended up shipping as is and did not have any problems upgrading in the field.
My issue was a combination of both changing distribution profiles and upgrading from the Hockey SDK -> App Center in the same build.
Anyone running into this using App Center. I suggest double checking if you have the issue on TestFlight.