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