Notes and Annotations disappear?

We have been using Charts/Music Stand for about 4 months now without any problems, but this week all our notes and annotations have disappeared. All we have are fresh, clean charts with no notes, etc. These are uploaded PDF's (Lead Sheets, Piano Accompaniment sheets, Vocal Charts). Any idea what could have caused this? If this continues to happen we will be forced to go to another program.

Annotations are saved per user and should not be deleted unless the user deletes them manually.

Are you signing in with the same login you usually log in with? Annotations cannot be shared with other users, so they would not see your annotations on their devices.
Alternatively, if multiple people share a user login, one of the users may have deleted the annotations, thus clearing them for everyone else using that login.