I think it will because Katherine was REALLY important in the two brother's lives. She was like their creator, soulmate and etc. So i think it will effect Elena's relationship with both brothers.
About the kiss.....as i'v said before in an ealier post...i think Damon had this doubts about Katherine being Elena after they're kiss because of the look his on face afterwards...or he could've been just surprised but there was something.....LOL Am i making any sense??