Messages that are stored in Exchange can be flagged in a number of ways to indicate different states to the user or as an effective method to prompt the user to action (or make them remember to do something).
The most commonly used Flag in Exchange is the Unread/Read Message flag which is used so when a message arrives in Mailbox a user can track which messages they have read. In EWS this flag is surfaced in the API in the form of a Strongly type property isRead https://msdn.microsoft.com/en-us/library/office/bb408987(v=exchg.150).aspx . (The underlying Store property that back this is PidTagMessageFlags property https://msdn.microsoft.com/en-us/library/ee160304(v=exchg.80).aspx which is a bitwise flag representing many states of a message).
The other place the Unread Message flag is surfaced is on the Folder object in the guise of the Unread Item count. So in the below example we Bind to Inbox folder and we can look at the Total Number of Items in a Folder and the Total number of those that are unread
Marking all Messages in a Folder Read
One of the new features added to EWS in 2013 was an operation that allows you to mark all messages as read in a folder. Also with the other important feature of being able to suppress Read Receipts when you do so. Eg the following is a function that will Mark all the Messages in a Folder as Read and Suppress Read Recipients.
Marking just one message as Read
To mark just the current message your enumerating in a function as Read as you need to do is use the isRead Strongly typed property eg the mark the last message received in a Mailbox read
All these example are in the following GitHub Script https://github.com/gscales/Powershell-Scripts/blob/master/unReadModule.ps1
Flagging a Message for Follow-up
Flagging a Message for follow-up is a common task you might do it to remind you that a message needs some other actions on it after you have read it (eg you need to phone the sender etc). In 2013 some strongly type properties where added to help read and set the follow-up flags. However these don't cover all the possible flag properties (listed here) you might want to set when setting a followup in particular the followup Text (eg the custom option in Outlook). To cater for this you can use a combination of Extended property's and the strongly typed properties. Eg To flag the last message with a follow-up to call the sender in 1 hour you can use the following
This example is covered in the following GitHub Script https://github.com/gscales/Powershell-Scripts/blob/master/flaggfollowup.ps1
Sender Flags are a more advanced Outlook feature that allows you to transmit a specific flag to a recipient with the message. There is no support in EWS for setting this type of flag but I have another workaround solution I've published before for this http://gsexdev.blogspot.com.au/2013/12/using-sender-flags-in-ews.html