My apologies if I am not understanding what you're saying. My question in this thread may not be very well worded.
I am able to see if all host-aliases that exist in file1 also exist in file2. The problem that I now face is that I need to know if the host-alias exists under the same "host id" in both files.
So, if host-alias www.foo.com exists under "host id" bobjones in file1, it also must exist under bobjones in file2. I hope that makes sense :)