At Eagle, lineholders get the credit for the flights they fatigued removed initially. Then the pilot submits a fatigue review form which is reviewed by the VP of flight ops and a union rep. If the fatigue is "justified" the pay is restored. ALL the people I know (including me) who have submitted a fatigue review have had their pay restored. It usually takes a month or two. Our CEO even wrote us a letter saying we need to take it upon ourselves to be removed from a flight if we are not fit.
For reserves, if you have flown over 3.9 hours and call in fatigued you have no pay/credit removed. If you have flown less than 3.9 you have to do the process above.