Q:Agreed that it is no longer valid to download the package but the it is already an active package how it can become Orphan when it is installed and assigned!!
A: This is what an orphaned package is. It is a package the device received and installed, however it no longer fixes the criteria to have that package installed. An orphaned package will not be removed unless you actively push down a update now and select the delete orphan option.
Q: Is there any other way to make the selection criteria where in I have different packages with Custom.Test set as 1,2,3,4,5 and I want to install 1 on store1 and 2 on store2 and so on. So if 1 is not installed on store 1 it will install the specific package and be active instead of Orphan.
A: If you wish for the package to be active after installation you need to ensure the device will fit the package criteria after it is installed. So if you have 5 unique packages and you set a custom property to uniquely identify the device you could just use the criteria of "Custom.Store=1", this would then install the package and stay active. Where you got in trouble was using the not.