We consider the task of effect estimation of resource allocation algorithms through clinical trials. Such algorithms are tasked with optimally utilizing severely limited intervention resources, with the goal of maximizing their overall benefits derived. Evaluation of such algorithms through clinical trials proves difficult, notwithstanding the scale of the trial, because the agents’ outcomes are inextricably linked through the budget constraint controlling the intervention decisions. Towards building more powerful estimators with improved statistical significance estimates, we propose a novel concept involving retrospective reshuffling of participants across experimental arms at the end of a clinical trial. We identify conditions under which such reassignments are permissible and can be leveraged to construct counterfactual clinical trials, whose outcomes can be accurately ‘observed’ without uncertainty, for free. We prove theoretically that such an estimator is more accurate than common estimators based on sample means — we show that it returns an unbiased estimate and simultaneously reduces variance. We demonstrate the value of our approach through empirical experiments on both, real case studies as well as synthetic and realistic data sets and show improved estimation accuracy across the board.