Actually, I'm not aware of that. I still think that "if Caesar kept his legions in one place out of fear that [x would happen]" is how the conditional is operating.
To be clear, the reason why I said you seemed to be aware of that is because you said that the
ne clause seems to be the apodosis of the conditional. That is completely incompatible with interpreting it as "If Caesar kept his legions in one place out of fear that [x would happen]," which would make the
ne clause a subordinate clause within the conditional.
Basically if we remove the
si clause entirely, the main structure of the sentence is:
Magnam haec res Caesari difficultatem ad consilium capiendum adferebat, ne cuncta Gallia deficeret. As Pacifica pointed out, the
ne clause "loosely explains what the 'difficulty' is." It's basically telling you what outcome Caesar is trying (with difficulty) to avoid. "This situation gave Caesar great difficulty in coming up with a plan, lest all of Gaul revolt." The
si clause has nothing to do with explaining the grammatical function of anything in that part of the sentence.
Now we can add in the
si clause. One way to interpret it is as logically a subordinate part of the
ne clause (i.e. "This situation gave Caesar great difficulty in coming up with a plan, lest, if he kept his legions in one place, all of Gaul revolt."). This would make it a pretty standard "future" conditional within reported thoughts (it's not an indirect statement, but the principle is the same; we're reporting Caesar's worries about what might happen if x happens).
You could also interpret it as a subordinate clause directly dependent on the main clause: "If Caesar were to keep his legions in one place, this situation was bringing Caesar great difficulty." Here it is the sort of future conditional retrojected into the past that we see in the first two examples of A&G §516 f.
My guess is that if you were to resurrect Caesar and ask him which it was, he wouldn't be able to answer; the meaning is basically the same either way, and it's a slightly loosely constructed sentence.