This typically happens when you log out of icloud for Windows or sometimes when you upgrade to a later version of icloud for Windows. The when you open Outlook you get that message. I answer "yes" to that question because when you log out and back into icloud for Windows, it sets up a new icloud calendar in Outlook and the question is directed to the former version of that calendar. They will likely both be the same and if you keep them both the older of the icloud calendars should end up under the My Calendars heading and the newer one under the iCloud heading in the Folder Pane. Also, when you log out and back into icloud for Windows, you should see your icloud contacts and calendars being uploaded from icloud. And when you get back into Outlook, your Code Two Sync settings should be blank (and you will need to re-enter the sync you want. What may be happening with you is because you kept the old calendar, Code Two is trying to sync with that old calendar which is now not connected to icloud anymore (because that connection was replaced by the new calendar created when you logged back in).
Take a look at which calendars are listed in the Folder pane in Outlook and under which headings. That might give you a clue as to what is going on. I think your best bet is to: 1) in Outlook create a dummy calendar under My Calendars; 2) in Outlook, copy all of the calendar entries from Calendar-icloud under the iCloud to the dummy calendar (this is to make sure you don't lose anything because when you log out of and back into icloud for Windows, all of the calendar entries in the calendar that you sync with the icloud calendar will disappear; 3) close Outlook; 4) log out of iCloud for windows; 5) log back into iCloud for windows and tick "Mail, Contacts, Calendars and Tasks with Outlook". You should see a status bar that shows items being downloaded from iCloud. If any message come up about keeping your icloud calendar in Outlook, click no; 6) re-open Outlook and if the message comes up about a folder being deleted, click yes to remove it from the programs setting.; 7) check in Outlook to see if the calendar under icloud has all you calendar entries; 8) check in Outlook to see if the calendar that you want to sync with the icloud calendar (not the dummy calendar you created in step 1) is empty (it should be). If it isn't but the icloud calendar does have them, then delete all of the entries in the sync calendar. Go into CodeTwo Settings from within Outlook and set up the two-way sync between the icloud calendar and your desired sync calendar. This should populate the sync calendar with all of the icloud calendar entries. If it all works, then you can delete the dummy calendar. If anything goes awry with the icloud clanedar, you can always use the dummy calendar to repopulate all of the entries into the icloud calendar. Hope this helps.