You may be hitting the note detailed in Step #2 below;
Step 1 After you complete the Cisco Unified Communications Manager upgrade process, navigate to Cisco Unified CallManager Administration and choose System > Licensing > License File Upload.
The License File Upload window displays.
Step 2 Choose the license XML file from the Existing Files drop-down list, and click View File. The window refreshes and displays the information for the selected license. Copy all of the information in this file except the HTML tags. To copy the contents on this window, choose the appropriate text and choose Ctrl-C (Copy).
"when you capture the xml file for the DLUS etc after the upgrade so that you can post it on Cisco's web site, it might be wrapped in HTML. ie the first line and the last line are html, and the license utility will reject it. Remove the first and last line to resolve this."
In addition to the great info from Rob (as usual +5) make sure you have processed the PUT order from 4.2 to 6.x so you get the feature license to actually activate the CM service on the new cluster. The XML file will get you your nodes and DLU's, but not the UCM 6 feature license.
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