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There is no problem to upgrade UPK 3.5.1 content to UPK 3.6.1 but it ever better to do a backup. If you use a multiple user install, backup the database. If you use a single user install, create the ODARC.
Just a question, why do you want to upgrade to version 3.6.1? For your information, the release 11.0 is available since 6 months and 11.1 since a week?
It is fairly straight-forward to upgrade from 3.5.x to 3.6. According to the upgrade guide (supplied with 3.6 install media), you can easily upgrade your virtual directory and the existing database, but your web server will need to be implemented in a new location.
Also check the references in the document to the following:
1. Publishing Styles
Customised Views and Permissions will be maintained for the upgrade (no changes required).
Focus on the following section in the Upgrade.pdf guide:
"Upgrade from 3.1.x, 3.5, or 3.5.1", then also look at the sub-section "Important Considerations before upgrading from 3.5.1"
Hope this helps you further.