Usually the rod cap bolts have a knurl on them which helps locate/align the cap and rod. If you replace the bolt, the new bolt may not locate exactly in the same location as the original one. This can cause a mis-match in the bore. Any mis'match in the bore, can cause a drag on the crank or even lock it up from turning altogether.
If you replace the bolts, it's best to re-machine the crank bore in the rod.