The conjunctive quod sī may be translated ‘but if’ or ‘if however,’ and generally modifies or qualifies a preceding statement with a new condition. It is therefore distinction from the isolate sī, which may produce conditionals without precedent.
If Caesar arrives, we are done for: sī Caesar veneat, pereāmus. (FLV construction)
If Caesar arrives, we are done for, but if we flee, we might survive: sī Caesar veneat, pereāmus, quod sī fugiāmus, fortasse vivāmus.
Caesar is coming. However, if we flee, we might survive: Caesar venit. Quod sī fugiāmus, fortasse vivāmus.
In short, quod sī establishes a conditional in direct relation to some other fact or some other conditional.