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This paper explores the time-modulated waveguide setups for unique and accurate permittivity and permeability extraction of lossy dispersive samples with phase-less measurements. We theoretically demonstrate that when the position of the short-circuit termination is dynamically modulated in a predefined way, the phase information of the reflection S-parameter manifests itself into the amplitude level of the emerging harmonics. Being insensitive to the calibration plane shifts and phase uncertainties in reflection measurements while bypassing a priori knowledge about the material under test (MUT) and also the transmission coefficient, can be enumerated as the main advantages of the proposed time-modulated retrieval scheme. Moreover, the presented reconstruction algorithm offers a simple post-processing step to facilitate fast computations of $\varepsilon_r$ and $μ_r$. Several illustrative examples at X-band frequencies have been presented to numerically verify the validity of the proposed approach for some applicable and practical types of homogeneous materials. Two possible realization and measurement configurations are suggested and discussed based on mechanical actuation and electrical phase control. We have also performed an uncertainty analysis to examine how the realization tolerances can affect the accuracy of results. By involving the temporal dimension, the proposed strategy takes a great step forwards in phase-less reconstruction of the electromagnetic parameters.