Here are the steps I used to solve this issue. It was a pain to do... I had to actually get Microsoft involved to solve this.
Step 1: Within PowerApps, export the application (I would have removed all data sources, since those could easily be reconnected later which is done at a later step.)
Step 2: Within PowerApps, go to each place in the code where Flows is called at then copy the code into a OneNote or Word document.
You will need to add these back in Step 15.
NOTE: When you add the Flows back it will delete the code. So you will need to save the code beforehand.
Step 3: In the file directory, rename the file from. MSAPP to .ZIP
Example: STASCMProjectTrackerApp20200605.msapp to STASCMProjectTrackerApp20200605.zip
NOTE: STASCMProjectTrackerApp20200605 is the name of the folder
Step 4: In the file directory, un-zip the file into a folder where the path does not have any spaces in it. Example: C:\Temp\
Step 5: In the file directory, find the Properties.Json file and open it up in NotePad.
Step 6: In the file directory, delete everything between "LocalConnectionReferences" and "LocalDatabaseReferences" leaving this instead "LocalConnectionReferences":"{}","LocalDatabaseReferences":"{}",
NOTE: All connection information between Flows and the Data Sources will be deleted. You will add it back in Steps 12, 13, and 14
Step 7: In the file directory, save the file
Step 8: Within PowerShell, go to the directory where the folder is located. The directory must not have any spaces in the path name.
Example: cd C:\temp\STASCMProjectTrackerApp20200605
Step 9: Within PowerShell, re-compress the folder into a new name
Example: C:\temp\STASCMProjectTrackerApp20200605> Compress-Archive -Path .\* -DestinationPath .\STACCMProjectTrackerApp20200605Mod.zip
NOTE: STACCMProjectTrackerApp20200605Mod is the new folder name
Step 10: In the file directory, re-name the compressed folder back to .MSAPP
Example: STACCMProjectTrackerApp20200605Mod.zip to STACCMProjectTrackerApp20200605Mod.msapp
Step 11: Within PowerApps, create a new application with a different name or you can use the existing application then upload the new folder: STACCMProjectTrackerApp20200605Mod.msapp
Step 12: Within PowerApps, remove all connected data sources and flows from the application.
Step 13: Within PowerApps, reconnect all data sources back to the application.
Step 14: Within PowerApps, add the Flows back to the application where it is called at which will delete the code then paste the code back in. Do this for each Flow that is called.
Step 15: Within PowerApps, save the application.
Step 16: Within PowerApps, test - close / re-open the application to see if you are still getting orphan connections. Check to see if the orphan flows still exist or not. Check to see if you can play the application. Check to see if you can publish and share the application. See if the shared user can open and play the application.
