A system and method are described for correcting for a loss of message boundary in a real-time data transmission over an interconnect between a source node and a destination node in an apparatus. In the apparatus, a destination node received one or more messages, wherein each message includes one or more data frames, and each data frame of each message includes an end-of-message flag and a message sequence number, the end-of-message flag set when the data frame is the last data frame in a particular message, and the message sequence number is different for different messages. A loss of message boundary is determined for a previous message when a new data frame of a new message is received and the new message sequence number of the new data frame is different from the previous message sequence number and a last received data frame did not include a set end-of-message flag. To establish re-synchronization, the destination node transmits a synchronization loss message to the source node, and the destination node receives in reply a status report message, and the destination node can regain synchronization of the last received message data such that a previous message boundary can be determined according to the status report message.