Currently looking for Confluence upgrade from v6.1.2 to v6.3 in our organization
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Yes, you might run into some. Depends on your setup, data and add-ons.
Try a test run, that will tell you what you need to know. Although a standard, no-add-on 6.1 to 6.3 seems to run flawlessly when I've tested it. (and 6.2 and 6.4)
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