When using Exchange, users may see an issue where some email messages that the user reads will delete from the device on the following sync cycle.
This is a known issue through Microsoft when the sender requests a read receipt. If the original sender requests a read receipt the Message ID assigned to the message changes when the receipient reads the message.
When this Message ID changes, NotifyLink sees this as a deleted item. A delete command is then sent down to the device if the user is set to "Sync Message Changes" in the Admin Console under User Administration -> Select the User -> User IT Policies -> Control Options
The work-around for this is to make sure the user is set to "Sync All Mail" in the Admin Console under User Administration -> Select the User -> User IT Policies -> Control Options. This will ensure that even though the Message ID changes and is deleted, it will still find the new Message ID for this message and send it down to the phone again.
As long as both Sync Message Changes and Sync All Mail are selected for users experiencing this problem everything should work properly for them.