You can even point your ER Compare to an older version OW if you point it to the proper spec directory. This helps make conversions pretty easy. If you copied a JDE program and now are upgrading. In the new environment Copy the JDE program again, use ER Compare to pull in your custom variable if you have any. Save, exit, then go back in. Then pull in your custom code. Then Test.
If you need something outside JDE for BSFN's. There is a program called Ultra Edit which is a really good text editor that can easily compare two source files. It has a lot of different options for the compare and color codes everything. It is very effective.
Rob