Ok so I want to start out with the standard Gregory calendar and then switch to a custom calendar, is that possible?
Help->Aeon Timeline Help includes a section on Calendars and Dates. The article How to Set up a Julian Calendar has some details.
Your ability to change calendar parameters is reduced once you have events or timeline markers in your file.
Exporting to CSV, then adjusting in your spreadsheet or with a wonderful product called Easy Data Transform, is probably also an option. You can import your modified data into a new Aeon file.
I ended up just making two save files since this was early in the story, on another note I would love an option to have participating character color make up an equal portion on the event circle like you gotta admit that would look so clean! 
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