During LID test measurements, modules are flash tested prior to undergoing light exposure, and the LID loss is relative to this flashed value. The input in PVsyst does not distinguish between the two; it just reduces your output by whatever value you input. So you can enter both values, the module quality adjustment based on FTD and the full LID value (standard practice), or add the module quality adjustment value to the LID loss and include as a single value in LID, setting MQF then to 0.
Thanks a lot for this reply. I have been having the same issue for a while. I will try out this and see if it will work