Advice Needed - Download Apps in Advance of Update
If you modify Profile A to contain Version 2 and then schedule the install of that Profile A the existing Version 1 will remain installed on the devices and untouched until that install window. This process will seamless remove Version 1 and allow Version 2 to be installed over top, maintaining and App Cache and Data, whereas your process will either end up in a situation where there is a conflict as you have seen or if it is successful then any App Cache or manually granted permissions you wanted to preserve through the upgrade would be wiped out. Modifying an existing Profile to change a package version (assuming you are also building from the same Package MCP and not creating a new one) is the way to go. The only catch to this is the fact that any net new devices enrolled that become eligible for Profile A during the period in which you have scheduled Version 2, will not get Version 1 or Version 2 because Version 1 is kind of in a disabled, but not deleted or revoked state while Version 2 is still scheduled.
You can also use the different scheduling options between Apply and Install to have the package actually downloaded to the device early but not activated until the install window occurs.
I headed down this path to begin with..... but ran into a couple of issues. What happens if you want to change the Install time? Again, thought I had it figured out (thought it was server time) but the device on the west coast didn't trigger when I expected. I really do want / need some flexibility and an just trying to figure out what works as all the documentation is sadly lacking.
I will need to do some more testing.