That's strange. Renewal shouldn't result in creation of new lineages (i.e. /etc/letsencrypt/{live,archive}/ directories) under any circumstances.
Things might go wrong if you modified files under /etc/letsencrypt/archive/ or /etc/letsencrypt/live/, but all bets are off if you do that.
Usually this will only happen in the set of circumstances described in this post.
Could you post that log file?