The flowline-based manufacturing system (FBMS) is a manufacturing environment wherein machines are arranged in the order in which jobs undergo operations, and jobs have an identical and uni-directional flow pattern. However, some or all jobs may not require processing on some machines. Scheduling of jobs in such a FBMS is considered in this paper with the focus on the development of non-permutation schedules. The significance of non-permutation schedules in improving the schedule performance measures, in the context of FBMS's, is first brought out. A heuristic procedure to derive non-permutation schedules from a given permutation schedule is subsequently proposed. The minimization of total flowtime of jobs is considered as the objective in the first instance, followed by the consideration of the minimization of total weighted flowtime of jobs. An extensive computational experimentation has been performed to evaluate the effectiveness of the proposed heuristic in improving the performance measures. Further, the performance of the proposed heuristic in generating non-permutation schedules has been compared with that of the benchmark dispatching rules namely, the SPT and SWPT rules.