I assume since it's in feet, you're working with State Plane Coordinate System, Lambert Conformal Conic Projection - which will introduce some area distortion but I doubt it would account for losing 29 acres, unless you are working way outside the standard parallels. Is this your projection, and are you within the standard parallels (e.g. the US)? If not, where is your area of interest and what projection are you using?
Other than that, I'd suggest looking closely at your before and after acreages to be certain the numbers are what they should be (e.g. was the before area calculated in a static field, then geometry changed?).