Anything that is placed into the camera’s optical path will degrade its performance. The extent of degradation depends on the protective window material composition. Even a properly designed window can affect image quality, and increase the amount of noise in low contrast scenes.
Any window material being considered should have better than 90% transmission, and have protective or anti-refection coatings designed for 8 to 14 micron wavelength light. Using a Germanium (Ge) window designed to operate in the longwave infrared portion of the spectrum (7.5 to 13.5 microns) should result in little loss of performance. If, however, a window made from standard silicon glass is used, very little thermal energy will pass through.
Edmund Optics is a recommended resource for IR-transparent windows. IR-transparent windows can be expensive, but perhaps less costly than having to replace the lens on the camera. An alternative window material to consider may be Zinc Selenide (ZnSe). It is less transmissive than Germanium, but also less expensive.
Please note that for FLIR camera modules with Radiometry and/or Advanced Radiometry options enabled, the use of a protective window will affect the temperature conversion accuracy, since the factory radiometric calibration does not take into account the possibility of a protective window being introduced.
Keywords: Tau2, Quark2, Boson