The effects of sequential cross-linking and scission of polymer networks formed in two states of strain are investigated using molecular dynamics simulations. Two-stage networks are studied in which a network formed in the unstrained state (stage 1) undergoes additional cross-linking in a uniaxially strained state (stage 2). The equilibrium stress is measured before and after removing some or all of the original (stage 1) cross-links. The results are interpreted in terms of a generalized independent network hypothesis. In networks where the first-stage cross-links are subsequently removed, a fraction (quantified by the stress transfer function Phi) of the second-stage cross-links contribute to the effective first-stage cross-link density. The stress transfer functions extracted from the MD simulations of the reacting networks are found to be in very good agreement with the predictions of Flory and Fricker. It was found that the fractional stress reduction upon removal of the first-stage cross-links could be accurately calculated from the slip tube model of Rubinstein and Panyukov modified to use the theoretical transfer functions of Fricker.