Apparatus and methods of recovering synchronization for multiple-link communications are disclosed. Streams of communication traffic on a plurality of communication links from which communication traffic is to be extracted and combined into a single communication traffic stream are monitored for receipt of synchronization information for each link. In the event that an error occurs in receipt of the synchronization information for any of the communication links, a stream received on each affected link is modified. For example, traffic may be removed from or inserted into a received stream where synchronization information for a link is received twice or received earlier than expected, respectively. If synchronization information for a link is missing, then it may be generated and inserted into the stream received on that link. In some embodiments, synchronization information includes sequence numbers, and inter-link synchronization is re-aligned to received sequence numbers when expected and received sequence numbers do not match.