The first few times I synced notes between my iPhone and Mac, however, I'd get a message like this one:
Since I don't have many notes on my iPhone to begin with, this alert would come up every time I changed, deleted, or added a note on the iPhone. This would also hold up completing the iPhone's sync with my Mac until I confirmed that syncing notes was okay.
After a few days of this, it was starting to get irritating. I racked my brain trying to figure out how to stop it.
Then I remembered: iSync is still its own program (though one largely restricted to the background these days), so there ought to be a preference in it to stop this behavior.
And there was. In iSync's preferences, you can set the threshold for the alert message that appears on syncing with your iPhone:
You can disable the alert entirely, or you can set it to go off if 50%, 25%, 5%, or any data on your Mac will be modified by syncing with the iPhone.
I'm not sure if this was set to 5% by default, or if years ago I'd set it that low out of paranoia and just forgot about it. Now I have it set at 50%, and the irritating alerts have gone away.