When using MS SQL Server as a source and the endpoint is configured to use "Start transactions in the database" on the Advanced settings > Prevent truncation of unread changes from TLOG, this requires the Log Reader Agent to be running to enable truncation of the Microsoft SQL Server active transaction log.
Note that if the Log Reader Agent is not running, the active log may become full, causing the source database to be essentially "read-only" until the issue is resolved.
If the log reader job is having issues and the log needs to be cleared up, the following manual 'emergency' procedure can be used so that Replicate will not miss any changes:
Stop the Log Reader SQL server agent job.
Run sp_repldone to mark everything as replicated: exec sp_repldone @xactid = NULL, @xact_seqno = NULL, @numtrans = 0, @time = 0, @reset = 1;
Execute a transaction log backup.
If the log reader job is running without error and the oldest transaction is moving forward then the log should be getting truncated when the backup runs.