Two points of clarification. If you do run the trace, leave the SHN Utility running as it is the one doing the actual xml tracing.
If you do the SYNCH EZSERVE to read the second PLM link database, upload a temporary devices3.xml file that has all the second PLM link definitions deleted. That way we can be sure any links that show up are from the second PLM database and not something left over from the devices3.xml. Of course save the original devices3.xml file with all the link information in case the SYNCH EZSERVE does not pull all the expected links back.