You can now remove a calendar from Keeper.sh after it has been deleted at the provider, including a calendar Keeper.sh writes into. Before this release, the dashboard hid the remove option for any calendar Keeper.sh writes into, so a deleted one stayed listed.
Keeper.sh still keeps you from removing a destination calendar that exists, because removing it could strand the copies it holds. That protection lifts once a refresh or the scheduled recheck finds the calendar is gone at the provider.
A removed calendar stays removed, and later refreshes do not bring it back. Keeper.sh also stops asking for change notifications from calendars that are gone.
Removing an account explains what happens to copies when you disconnect a calendar service.