Yes, you have to modify your pluhnews php files and replace all the lines containing links.
For example, a link to a thread in vb 2 was :
http://path_to_your_forum/showthread.php?s=Array[sessionhash]&threadid=xxxx
In vb 3, links to threads are now like this
http://path_to_your_forum/showthread.php?t=xxxx
So just search for lines containing "threadid=", remove "s=....." and change "threadid=" to "t="
It's simple, but if you don't succeed in it, I can send you my files.