You should remove any code that deletes function checks, since the presence of the indicator, 'E' extender, or *PSSR will prevent function checks from occurring.
When this program is converted to RPG IV, the layout of storage may be different, so that the corrupted storage is used by the program. This can cause an unexpected exception to occur, for example exception MCH3601 on a file operation such as a SETLL. If you experience mysterious errors that seem unrelated to your application, you should check the parameters of all your call operations to ensure the parameters all have the correct length.