Variables are-
Stroke and piston pin height
HOWEVER, you now have a lower compression ratio.
The compression ratio doesn't have to be different unless the specific substitutions (O.E. pistons I assume?) don't provide for equality.
The O.P.'s inquiry is interesting, but probably needs better definition of context in order to answer, and probably few from this vantage point could probably answer the question assuredly anyway, as this would for a truly accurate response require one (or more) of the engineers at Caterpillar familiar with this engine series to participate.
But, (now for the truly unknowledgeable response!
) if the compression ratio remains similar, with not a great piston dome configuration difference; with the same cylinder heads, with port flows and combustion chamber configurations the same; valve motion events consistent; the rod length is the same but the stroke is shorter so the rod to stroke ratio does change, but common, not that greatly; and with the shorter stroke (7.2" vs 6.75") which equals approximately 94% of what it was; and realizing that for the most part as another pointed out that diesels generally present un-throttled cylinder volumes in excess of the fuel supply; why wouldn't it work?
Well, yes technically, the engineers would find fault; the guys over at the E.P.A. would toss a fit, and yes some tailoring probably could make it better; but I'd bet it'd run, and as being one the things one does in 'hopping-up' a diesel is to 'turn-up' the fuel (which is sorta what would be happening here as the fuel delivery would remain constant but the capacity went down) depending on where CAT left off it might not take such a hit, performance wise, with the stroke loss, at least perhaps from a seat of the pants impression anyway?
But, then these are thoughts from the performance oriented perspective, where we all think we can make it run better than the engineers could anyway!
Scott.