Thanks I'll give it a try. One other wierd thing is that in this attached jpg you will notice the line at the bottom. This is our new ethernet network. Notice that some routers are shown red dotted as you indicated to the old frame and a solid red line to the new network. I can get to the router of course but according to this diagram they are off line.

The thick black line represents an ethernet bus. This indicates there are multiple CDP neighbors connected to a single interface on a device. This could also point to a CDP inconsistency on a certain device. The fact the the connecting links are red (as well as the devices) points to those devices not being SNMP reachable.

At this point, given the scope of your topology change, you might find it easier to reinitialize your ANI database, and perform a new Campus Data Collection to get a cleaner topology map. The topology can be reinitialized using the command:

NMSROOT/bin/perl NMSROOT/campus/bin/reinitdb.pl

Is that the UNIX command? I am running windows version and it just brings up a text file script.

That command will work on Windows, too, provided you change the slashes. Make sure you typed it correctly:

NMSROOT\bin\perl.exe NMSROOT\campus\bin\reinitdb.pl