The key detail for me is that if you delete the call from the log on any device, the next sync will delete it in iCloud.
I highly doubt that it is a hard deletion of data. My guess is that it would be a soft delete, so your call log won't show up on your iPhone, but the data will be retained on Apple's servers.
One way call logs will disappear from the cloud is if a user deletes a particular call record from the log on their device; then it will also get deleted from their iCloud account during the next automatic synchronization.
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I highly doubt that it is a hard deletion of data. My guess is that it would be a soft delete, so your call log won't show up on your iPhone, but the data will be retained on Apple's servers.
I'm just going by the article:
Does apple delete it from all their backups as well?
No worries, the NSA keeps a copy for you.
But does it get deleted, or marked as deleted?