We analyze the transmission characteristics of a Sagnac loop interferometer containing a polarization-dependent loss element and lossless polarization-converting elements by use of Jones matrices. We show that polarization independence in the transmission mode can be achieved in such a configuration and that maximum transmittance occurs when a half-wave plate is used for the polarization-converting element. The result is verified experimentally for a fiber acousto-optic tunable filter and cascaded long-period fiber gratings with either intrinsic or process-induced polarization-dependent filtering characteristics.