I performed an in-place test upgrade of my 6.0 Author and Publish servers (two separate servers with the standard ports of 4502 and 4503 respectively) to 6.1. We were already on the new crx3 instead of crx2 since the 6.0 servers were brand new. The Author server did just fine, all my content is there. However, my Publish server seems to have wiped out all the content, dam, and apps - it did leave the custom map.publish script in place as well as custom packages, so it didn't appear to completely wipe out the old installation. I tried the upgrade first by renaming the AEM_6.1_Quickstart file to cq5-publish-p4503 (the same as the old jar file) with this result. Then I brought up another clone of the server and did the command line upgrade (java -jar aem_6.1_quickstart -r publish) with the same result. The Upgrade log files show that it was performing an upgrade and not a fresh install. As we have 3 large websites and don't want to have to push all those pages and images from Author to Publish, I'd like to know if anyone has any ideas. I have a fresh clone standing by.
