I am writing a program for a 1768 CompactLogix 5343 Controller communicating with two flex I/O stations due to lack of space in the control room. It was brought to my attention that I may need to download it into the flex stations as well. Is this true?

 

If it is already running you won't likely have to do anything with the flex I/O.

With new modules sometimes you need to load firmware or set addresses, but if it is already running it should be fine.