Hi Sebastian,
It should be possible to control this kind of material properties during simulation run-time using the EnergyManagementSystem:ConstructionIndexVariable object in EMS.
You can refer to the following publication, or contact Fabio, for more information about a recent application of this modeling approach:Â
Fabio Favoino, Mauro Overend, Qian Jin, The optimal thermo-optical properties and energy saving potential of adaptive glazing technologies, Applied Energy, Volume 156, 15 October 2015, Pages 1-15,Â
http://dx.doi.org/10.1016/j.apenergy.2015.05.065.
You raise an important point with respect to the correct treatment of thermal history effects in the simulation process of facades with dynamic thermophysical properties.
In a recent article, we have demonstrated that such effects can play a dominant role, especially when it comes to adaptability  of heavyweight constructions (for dynamic fenestration systems, though, this effect may be negligible):  Loonen, R.C.G.M., Hoes, P. & Hensen, J.L.M. (2014). Performance prediction of buildings with responsive building elements: challenges and solutions. In Proceedings of the 2014 Building Simulation and Optimization Conference (BSO14):Â
http://repository.tue.nl/776507
As far as I am aware, it is not possible to overwrite initial state values in EnergyPlus. Although it is rather complex, the use of an initialization horizon can be a solution. See also:Â Coffey, B. (2013). Approximating model predictive control with existing building simulation tools and offline optimization. Journal of Building Performance Simulation, 6(3), 220-235.
Best regards,
Roel Loonen
Eindhoven University of Technology