When organising my iCal calendars (post iClouding them) and attempting to merge two calendars together, I found iCal would add them but then during the "updating.." process it would delete each event - leaving you with a empty calendar at the end of it.
I eventually resolved this using the following process:
WARNING: As always when messing about with important data. Make sure you back everything up. Exporting all your calendars should be enough. But possibly research other iCal backup techniques.
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Right click and export each iCloud calendar that you eventually want to merge.
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Create a new local calendar: File > New Calendar > On My Mac
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Double click each ics file that you exported. It will prompt you for a destination calendar. Choose your new calendar.
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Now that you have your local calendar with all merged events. Open System Preferences > iCloud. Uncheck the Calendars item. It will say "Delete from My Mac (but everything is safe online)". Proceed to do that.
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After that has finished updating. Recheck the Calendars item and let it merge your local calendars into iCloud. Your new calendar should now be in the cloud :)
References:
https://discussions.apple.com/thread/3375438?start=0&tstart=0