Customized environments require additional attention during an upgrade. The instructions in upgrade manual assume that you have followed the standards for customizing Oracle E-Business Suite as described in the Oracle E-Business Suite Developer's Guide and the Oracle E-Business Suite User Interface Standards for Forms-based Products.
Developing and Deploying Customizations in Oracle E-Business Suite Release 12.2 (Doc ID 1577661.1)
Useful 12.2 Documents For Customers And ATG Support Engineers (Doc ID 1585889.1) -- Customizations
Please follow the docs/links above to avoid losing any customizations during the upgrade.
My previous update was for 12.2 upgrade, my bad
If you are looking for 12.1.x please see:
Prepare an upgrade plan for customizations (conditional)