AFAIK replay files don't save data directly relating to unit stats, so if you create a replay, then mod the unit data, then play the replay things will get very odd very quickly. The replay will soon "get out of step" if the unit data has changed, because, for example, all the combat calculations are being done while the replay is in progress. Modded units won't produce the same results.

Providing that nothing changes between recording and replay everything should be OK, as you'd expect.