After a short reading the FM: There are no conections between the NBC System an the FCS.
This System contents of two Parts, One is the Overpressure and Filter System. This System gets contaminated Air over 3 Filters in to the Tank and produces a Overpressure of 4 mBar (or 4 cm water column, its nice at rainy conditions too)
The other Part is the so called Auflauframpe, that is the mechanism that open the Breech after firing a Round, this mechanism can be switched off.
Loading Position is activated by a Switch called "Rohr vorn" (Gun Front). So, even under NBC Conditions the FCS must go into Loading Position if Breech opens or not.