Catalysis of site-specific recombination is preceded by the formation of a synapse comprising two DNA sites and multiple subunits of the recombinase, together with other "accessory" proteins in some cases. We investigated the stability of synapses of Tn3 resolvase-bound res recombination sites, in plasmids containing either two or three res sites. Although synapses are long-lived in plasmids with just two res sites, persisting for tens of minutes, a synapse of any two sites is relatively short-lived in plasmids with three res sites. The three alternative pairwise synapses that can be formed in three-res plasmids re-assort rapidly relative to the rate of recombination. We propose a "partner exchange" mechanism for this re-assortment, involving direct attack on a synapse by an unpaired res site. This mechanism reconciles studies on selective synapsis in multi-res substrates, which imply rapid interchange of synaptic pairings, with studies indicating that synapses of two Tn3res sites are stable.