If you delete entries in your Org files, the corresponding iCalendar
entries will by default get deleted. You can change that behavior with
org-caldav-delete-calendar-entries to never delete, or to ask before
deletion.
You must be careful to not simply remove previously synced files from
org-caldav-files, as org-caldav would view all the entries from those
files as deleted and hence by default also delete them from the
calendar. However, org-caldav should be able to detect this situation
and warn you with the message ’Previously synced file(s) are missing’,
asking you whether to continue nonetheless.
If you delete events in your calendar, you will by default get asked
if you’d like to delete the corresponding Org event. You can change
that behavior through org-caldav-delete-org-entries.
If you answer a deletion request with "no", the event should get
re-synced to the calendar next time you call org-caldav-sync.