Cut and Run
The best practice for incorporating incoming email into your applications is to get the message out of the email layer as quickly as possible and into a transaction that can be controlled more tightly. The mailbox should never be used as a receptacle for data related to an ongoing process. Instead, the mail should be read out as quickly as possible and loaded into another queue. A database is an obvious choice here.
When retrieving messages, log in, do your business, and log out as quickly as possible. Staying connected and periodically polling for new messages consumes network resources, which is reason enough to try and avoid doing this, but this also makes it much more difficult to write code that will properly handle dropped connections to the mail server.
Connecting to most well-written servers will obtain a lock on the mailbox. If there is any possibility at all that more than one thread (or more than one application) will access a mailbox at the same time, each thread or application should be aware of the possibility of conflict, and should fail gracefully when this happens. For the same reason, applications should be sure to close connections as soon as possible to free up access to the resource. If this can be avoided, so much the better.
Needless to say, information about the state of a mailbox should be considered out-of-date as soon as the connection to the mailbox is closed. This is particularly true of the message IDs provided by the message store, which ...