Keep in mind that the appraisal measurements are not supposed to be to the exact square footage. You aren't indicating that, but I'm just making sure. Assuming that the market is similar to mine, and it may not be, but the differences in the first appraisers measurements are about 6%. The question is, and this is assuming that the 3,750 is accurate, how much damage have you actually incurred? In my market, location is far more of an indicator of value than square footage. In my market, the difference between a 3,978 and a 3,750, as long as everything else is the same is minimal. However, there is a difference. You may want to hire a third party certified appraiser to ascertain that difference.
Also, the latest appraisal of 613 square feet difference is substantial. That appraiser may or may not be right. An engineer may be able to get you a more accurate square footage, just make sure they use the same standards. That will cost you money. If the latest appraiser is wrong, you have suffered damages as well. That may be more significant. You will have to do your homework to see who screwed up, and then how much it cost you.