Hi ProblemMan,
Do you have DAG in-place, make sure replication is fine and there are no issues with the passive copies. Truncation would not happen if passive copies are failing.
"the transaction logs couldn't be flushed" are you forcing it somehow or just saying its not getting flushed as usual.
If the mailbox database is replicated, it will use continuous replication circular logging (CRCL). In this case, enabling or disabling CRCL takes effect dynamically; there is no need to dismount and re-mount the database.
Circular Logging and Mailbox Database Copies: (Article is bit old, but you get the idea.)
Configure circular logging for a mailbox database:
https://technet.microsoft.com/en-us/library/dn756374(v=exchg.150).aspx
Make sure these services are running without any errors:
Whereas ESE circular logging is performed and managed by the Microsoft Exchange Information Store service, CRCL is performed and managed by the Microsoft Exchange Replication service