First, you should upgrade to CM 5.0.5 and DFM 3.0.5, especially if this is a Windows server.
To reinitialize the topology portion of the ANI database, run:
NMSROOT/bin/perl NMSROOT/campus/bin/reinitdb.pl
After that, there will be no more layer 2 topology. You can then run a fresh Data Collection to repopulate.