Ink Calendar uses OneDrive to sync ink across devices. This means all of the data is stored and transmitted with OneDrive services. Ink is not stored or transmitted in any other way.
When merging ink the latest ink file always takes precedence. During the initial sync which ever file was edited last will be the ink file which is uploaded to OneDrive and will overwrite all other ink files.
To avoid possible loss of ink backup all ink before signing in with a Microsoft Account. An easy way to mark a file as the one which you want to keep would be to make a small mark on that view to set the modified date to a more recent time.
If you have any issues with ink syncing please email support at inkcalendar dot com.