If you are simply altering the leg then there shouldnt be any problem overall, its just some people alter the waist and the leg width and that really knackers them up LOL. Most guys just cuff the jeans anyway to shorten them and as a stylistic choice which shows off the genuine selvedge to all those haters out there who think you are wearing fakes

LOL. If there is simply too much to cuff then by all means shorten the leg, after all, they are your jeans, but bear in mind its unlikely that you will find anyone local who can re create the original chainstich at the hem. It will just be a simple single stitch which wont look as good and will almost cetainly devalue the jeans should you decide to sell them again.