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Cooperative communication systems have attracted much attention recently due to their desirable performance gain while using single antenna terminals. This paper addresses the joint timing and channel estimation problem, and furthermore the resynchronization of multiple timing offsets in a cooperative relay system. The estimations of timing and channel are conducted in two phases and the associated Cramer-Rao bounds (CRB) are derived for both phases. It is demonstrated that the conventional CRB is not valid for timing parameters under fading conditions, and a new bound called weighted Bayesian CRB is proposed. With the timing and channel estimates, a general framework of the resynchronization filter design is developed in order to compensate the multiple timing offsets at the destination. The proposed methods are applied to different scenarios with varying degrees of timing misalignment and are numerically shown to provide excellent performances that approach the perfectly synchronized case.