Not a big deal. In fact it is recommend to flip the rods after a rebuild. Check the rod tips and one end will have a slightly fatter rounder end than the other. This fatter rounder end is to be inserted up and into to rocker. This comes from "How to build a Ford engine" manual.
It is important to keep the rods and pistons in order if you plan on re-using them. Also the Lifters should be kept in order if you are going to use the same cam and lifters. If you are keeping the cam and did not keep the lifters in order or you are installing a new cam then you should buy new lifters. Reason is the lifters are broke in to the shape of the cam lobe.
