R3 Upgrade: The code upgrade - don't forget to Run code upgrade checklist!
In my prior AX Upgrade post, R3 Upgrade journey - creating the R3 environment, I referenced the Upgrade in-place technet Article. The article details out a long and arduous procedure, it is packed full of information and steps for the system administrator to follow. It also directs you to several other articles. When doing the code upgrade, you need to run the code upgrade checklist after applying each model.
From the Upgrade in-place technet Article
This is very critical to insure that any new objects being defined will carry across to the R3 environment. In particular any new custom tables - it is VERY, VERY important and will affect your data upgrade!!! The technical lingo and pointer to the technet article is "preserve legacy element IDs [AX 2012]" when upgrading. If you miss this step, you will lose the Business Data that are in these tables. You will have to start over with applying code layer by layer. This is because R2 added a column, partition, to all tables so you won't be able to copy the table over using SQL "select into" command. Refer to technet article Data partitioning architecture [AX 2012] for more information.