To answer the original question; no the dispute is not over. It has moved, hopefully, into another phase; genuine negotiation.
Whether this phase is the beginning of the end or the end of the beginning remains to be seen.
As to the 49ers; nothing has changed. The resinstatement of the 49ers was never a pre-condition to talks. Reinstatement was going to be on the agenda of any such talks and there can be no doubt that some mechanism that allows for a fair resolution to the issue of the 49ers will be a cornerstone of the forth-coming talks.