Okay, I use windows live messenger but I don't know which version it is. I tried finding a forum for it but all I could find is this.
I always save my chat history and I was merging one of my contact's log as I think it got split up while I was chatting and moving the location of the folder and changing where the message should be saved.
So I was chatting with my friend. Closed the window and went out. Came back home and was chatting again. Found out that the message history log of the previous conversation was in another location. Found this http://msnhistorymerger.codeplex.com/ and merged the conversations together and it worked.
But here's the problem - I was chatting all along while merging the log after I came back home and I just finished chatting but I found out that even though the chat window shows my last message, when i open the XML document of that particular contact, it shows the last message of the previous chat window which was before i went out. Why is this happening?

Because you were manipulating the files (merging) while those files were in use by Messenger.


Messenger probably saw that those files couldn't be accessed and as such created another new log, and/or you saved the merged log with the wrong name and/or to the wrong location, and/or you forgot to remove the partial source files of the merged log.


If you want to merge files (and this general rule of thumb goes for any files for any program, not just Messenger):
1) close all the programs which use those files before you start merging. In this case Messenger.
2) make sure the final file is saved in the correct location with the correct file name and correct file extension,
3) make sure you remove the partial files after the merging to avoid accidently continuing in an old partial file.