Think of the merge as a container. Thats all it is. A few different accounts/user names under one roof.
So I could have Joeuser on skype, joeuser on gtalk, and joeuser on sip.
They are all the same user, just different services.
When you merge them it just consolidates. It does not change any of the user info.
So when you look in your contacts book you will see the the user name. (the container) When you click on the user you will see the different service that user is on. (Skype/Gtalk/Sip) They are still separate services.
However if you click a contact and you "have two way sync" it will delete it from the server. Like I said. Skype is two way. Think of the n900 as your pc. The n900 will react the same way your PC will.

So as for your question...."if i merged a contact in n900 will not change my contact info in skype on PC" no because you are not modifying the skype account. You are creating a container locally on the n900.
When you delete a merged user (You will be deleting a container and everything in it)
Does that make sense or did I confuse you more....Sorry, but I'm not very good at verbalizing how things work.