Only Lionel knows for sure what changed between Rev. 1 and Rev. 2 of the RS-Lite boards. However, I can say with about 99.98% certainty that swapping them won't damage them. You may not get the exact results you seek, but you can always swap them back. I've swapped various versions of RS-Lite boards around without any issues.
The "sound chip" is actually a FLASH memory, the RS-Lite boards are factory programmed to the application, so all the boards from a specific run are identical hardware wise. The only issue I see is the possibility the serial data commands for sound have been altered in the intervening two years, but I tend to doubt that. They guy that could certainly say for sure what the risks are would be Jon Z. @SantaFeFan, he's the authority on these having been the designer of both ends.