This applies to the Windows Store and Windows Dev Center as of March 1, 2016 and assumes you are uploading a Windows 10 Universal Platform App.
The Windows Dev Center started out badly back in Windows 8, and it hasn’t improved too much since then. I have to be honest when I describe it, because it’s sometimes nothing short of painful. One of those pain points is the UI and poor documentation regarding the concept of the “App Name”.
In order to submit to the store, you need to create “App Packages”. Each package has metadata associated with it that you define in your “App Manifest” (Package.appxmanifest in your project). This manifest is where the app’s name must match exactly with whatever names you have reserved in your Dev Center for that app.
Creating the App Name
When you create an app submission, you have to pick an “App Name”. This is the name that is displayed across your Dev Center Dashboard and the Windows Store. This name also has to match exactly in your app’s created manifest. That secret bit of information isn’t documented well and seems to only appear in tiny text when you are creating an app package through Visual Studio.
Changing the App Name
If your app has not yet been submitted to the store, then you can change the name by reserving a new one in the Dev Center, changing the manifest to that name, creating an app package, and then uploading that package. Don’t try to rename directly from the Dev Center (that’s where I kept looking). Instead, you have to reserve the name and change it in the manifest to match. There is no way to rename an app from the Dev Center!
If your app has already been submitted, you will need to reserve the new name, create a new update submission, change the manifest accordingly, create the package, and upload it to the new submission. If the submission is approved, the new name should show up in the store. I think there’s a delay in the new name showing up (16-24 hours).