If you have a cloud account (Box, Dropbox, Google Drive, OneDrive) that is being shared by multiple iAnnotate users, some additional steps may need to be taken in order to ensure that one person's annotations on a particular document(s) don't overwrite the annotations made by others.
For example, if all users are marking up MeetingMinutes1.pdf, and each user tries to sync her annotations with the linked account, then the most recent set of changes will always overwrite the others and nullify that work.
There are a couple of options for preventing this issue:
Copying to Local Files Before Annotating
Select a downloaded document in your connection folder and tap Copy. Select "Local Files" > "Copy to 'Local Files'" to create a local copy of that document in the iAnnotate Library. That copied version is stored directly on the iPad and any changes made to it will not be uploaded back to the shared cloud account.
Connect as Read Only
Upon first creating a cloud-service connection, you can choose to set the connection as "Read Only." This means you can only download files from that connection; none of the annotations made to documents in that connection will be uploaded back to the server. If you're connecting to a shared connection, we highly recommend using Read Only to avoid over-writing other users' work, or making your own work public unintentionally.