It sounds as though the project will cost $560k and the FHA appraisal came in at $550K and you are concerned that the other appraisals are more accurate, and lower, by a significant amount. THAT sounds fishy. You need to look closely at all the appraisals. Make sure the comparable sales were all lakefront property, and if not, that an appropriate increase in value was added. Make sure they got the style of home correct, and that the square footage is comparable. Make sure the comps were new construction or that an appropriate increase in value was added to account for that as well. Make sure the comparable sales had upgrades comparable to yours or that an appropriate increase in value was added. All these factors weigh on a home's value
I had this happen last year to a lakefront owner for a refinance, the appraiser was from out of the area and used comps that either were not lake front at all or were on a small tributary, not on the main lake, and thus his opinion of value was so far off it was ridiculous. In fact, my clients actually reported him to the State Attorney General's office for over all incompetence. An appraisal is an opinion of value. That's all. Values go up and down and change based on a lot of factors, but I will tell you this, lake front property tends to hold its value better than most other property so make absolutely sure EVERYONE used comparable sales of LAKEFRONT property only and on the correct lake!