The new upgrade guide has been released at http://www.microsoft.com/en-us/download/details.aspx?id=14599 and has very detailed steps on performing an in-place upgrade of AX 2012/AX 2012 FP to AX 2012 R2. Download a copy and ensure it is dated December 2012.
It talks about all the steps you need to take, starting from creating a test system first and restoring a copy of your production database on to it and onwards. It suggests following the steps in the order given and makes several suggestions and recommendations to ensure a good upgrade path.