This is called "User Personalization" and is a function of AX's Intellimorph.
When you make changes to your form, the changes are packed and saved in a table called SysLastValue
which stores your user-specific usage data. When you open a form, it unpacks the saved settings that specifically match whatever form you are using.
When you upgraded from AX 2012 to AX 2012 R2, the form likely changed and has extra fields or something. Well when AX tries to unpack your saved usage data, the packed data doesn't match how it's now expecting it to be unpacked...so it doesn't work.
So what you need to do is make your changes again and then those will replace the old changes and should persist. If the form is modified in the future, or you clear your usage data (which empties the SysLastValue table for your user), you might run into the same issue with your personalization missing.
If there is a lot of personalization or the personalization is a common change for all users, then you should consider having a developer make these changes permanently on the form.