I've been having this problem for probably about a year now, and I have no idea why.
I like having a default calendar alert, and I do use them. However for many of my repeating calendar events, I don't want the default alert, instead wanting only to be notified at the time of the event, for example.
So on those events, I change the default alert value to "none", and when prompted if I want to save for all future events, I say yes.
If I then edit the event, I can confirm visually that the alert has been changed. I can quit Calendar, re-open it, and again confirm that the former default alert is now set to "none".
But then if the event is more than a couple of hours away (like the next day for instance), the default alert will be back. For all future events.
I do use iCloud calendars between my iMac (macOS Sierra), Macbook (High Sierra), and iPhone (iOS 11.3), and it doesn't matter which device I make the change on, it will always revert.
This is seriously annoying, does anyone know why this happens and how to fix it?