Cris and Seb? Not a problem. Cristian and Sebastian? Not a problem either; more of a theme or even a coincidence. The only thing you couldn't do would be to nickname one or both of them Tian.
I know a Rosalind who was about ten when her sister was born and named Rosemary. Their parents apologised for what they knew would lead to confusion, but pointed out that Rosemary had been born on their wedding anniversary: "Here's Rosemary; that's for remembrance: pray, love, remember". And in fact, she said, it hardly mattered and people hardly noticed. So if they could get away with the stressed syllables, you can surely manage the unstressed!