I've done that numerous times with no ramifications. Remember two things:

The FAA says only the pilot can determine if he is fit for duty. If you determine you are good to go for one leg, but not the rest of the trip, that is your call and your call alone.

You are doing crew sked and your company a huge favor by giving them a heads up and getting the airplane to a crew base where they can cover the trip with very little heartburn.

Personally, I have never been questioned about any sick call, much less one of these.