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.
Thank you, Anup!
I will have a closer look on this documented. Already attempted and upgrade from AX2012 RTM CU4 and it wasn't exactly a great experience. Several discrepancies compared to the instructions and guides I had at hand. Merry Xmas!
A newer version of the documentation for specifically the AX 2012 to Ax 2012 R2 in-place upgrade is published on TechNet and will make its way into the next version of the Upgrade guide when it is republished soon. Until the full upgrade guide is republished, look here for the updated documentation: technet.microsoft.com/.../jj733502.aspx