When uninstall Apollo 2015/2016, if user choose to "remove configuration" option, Apollo uninstaller will still leave some trash behind (e.g., registry keys, folders). User need to manually delete them.
Here is the list to check:
After Apollo Uninstallation
 Remove Files and Folders if there is any
Make sure to remove the following folders.
C:\Program Files\Hexagon\ERDAS APOLLO\
C:\Program Files\Common Files\Hexagon\Administration Console Service
C:\Program Files\Common Files\Hexagon\Services\
NOTE: if you have your own portal & layout you want to save, then don't delete this C:\Program Files\Common Files\Hexagon\Services\Instances\<YourPortal>
You should use the Configuration Update Utility first before upgrade:
Upgrading to 2016 at least for Geospatial Portal will not remove existing instances. After the upgrade is complete the existing instances will appear in Admin console with option to upgrade.
In this case it is not always necessary to upgrade, it could stay on old version. Here is an example of a recent upgrade to 2016 I carried out with new and old instances still very much intact.
If you want to be absolutely sure not to lose your instance you could copy and paste the folder from 2015 to the new 2016 location, but I don’t believe it would be necessary.
 Remove Registry Entries if there is any
1. There are several Registry keys that remain after the Uninstall, but the main one to be concerned with is HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Intergraph\Geospatial Server\Instances\apollo-portal. Using the Registry Editor, locate this key and delete it.
2. You can also delete the following keys, but these should not impact future installations.
HKEY_LOCAL_MACHINE\SOFTWARE\ERDAS\Image Web Server
HKEY_LOCAL_MACHINE\SOFTWARE\Intergraph\ERDAS APOLLO 2015
HKEY_LOCAL_MACHINE\SOFTWARE\Intergraph\ERDAS APOLLO Essentials
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\ERDAS\Image Web Server
 Remove IIS Configurations if there is any
Using the Administrative Tools > Internet Information Services command, select and expand Default Web Site in the tree view.
If any of the following virtual folders remain (aspnet_client should remain) remove them by right-clicking the item in the tree view, then selecting Remove.
NOTE: if you can not delete "AdminConsole", you can delete C:\inetpub\wwwroot\AdminConsole\ folder, then refresh "Default Web Site"
 Remove Apollo related App pool from IIS application Pools if there is any:
ERDAS APOLLO Essential
 Check services, make sure there is no JBOSS, Tomcat Smartsync ... services
If they still exist, then search registry and delete related keys
below are the keywords: