Your knowledge of portupgrade seems rather incomplete. I'd suggest you read this first:
http://www.onlamp.com/pub/a/bsd/2003...SD_Basics.html
One rule of thumb is *never* to force the upgrade to all your ports. You just are asking for trouble. It is better to do it in bunches, making sure always to read /usr/ports/UPDATING first.
Regarding your question, I'd guess that you have updated you ports tree, and things have moved around somewhat. That is no big deal, but you do have to update the ports databases so that the dependencies you need are handled properly.
You might also consider using "script" to record what happened. The files can be huge, but that is the only way you can wade through what happens if you do a large portupgrade.