3 days has past since the OP first asked the question so hopefully this still can be useful. I'm a Realtor and Investor so I see both sides of this and low appraisals have unfortunately been a common obstacle especially in flips. I've fought probably a dozen or so appraisals in my career and won 3 of them. Most people will just go back to the appraiser with different comps and in my experience this never works. What you need to do is get a copy of the appraisal report and dissect it completely. These reports are long and in most cases you can find at least 1 factual error. It doesn't matter what the error is, it can be anything from incorrect square footage on the subject property (or any of the comps) to having a comp incorrectly labeled as having lake privileges. The appraiser has an obligation to fix factual errors, they do not have an obligation to swap out comps. Once you find a factual error, it opens the door to you presenting alternative comps. Here's an example of an email I sent that I was successful in getting an appraisal challenged...hope it helps....
To whom it may concern, In response to the appraisal on XXXX Woodlawn St. I would like to point several factual errors that in my opinion should open the door for a review and challenge of the value submitted by the Appraiser.
Factual error #1 - In a recap of the contract, Appraiser notes there is "No" financial assistance provided to buyer. This is incorrect. There was a negotiated concession of $4,500. While this does not impact the opinion of value, it is incorrect and should be noted in a new appraisal.
Factual error #2 - Included Appliances. Appraiser correctly notes the Microwave, Disposal and dishwasher but failed to include Refrigerator, Stove/Range, Washer, Dryer. While this shouldn't have an direct impact on opinion of value, it is incorrect and should be noted in a new appraisal.
Factual error #3 - Comp 1 (216020389) is listed on the appraisal report as having lake privileges. This is incorrect. This factual error impacts the value of property directly and should be adjusted or the comp should be omitted and replaced with a comparable more in line with the subject property.
Factual error #4 - Comp 2 (216011175) is listed on the appraisal report as having lake privileges. This is incorrect. This factual error impacts the value of property directly and should be adjusted or the comp should be omitted and replaced with a comparable more in line with the subject property.
Factual Omission - Appraisal fails to credit subject property with a Shed (located behind the garage).
Other observations:
Comp #1 used in the appraisal should be eliminated completely. Comp #1 does NOT have lake privileges (subject property does), does not have a garage (subject property does), has a basement (subject property on a crawl) and does not have any porch, deck or patio (subject property has a wrap around porch).
Comp #1 is in inferior condition. There is no adjustment made for "Quality of construction." This is easily observed from the pictures in the listing. The kitchen in comparison to the subject property is inferior both in updates and size (10x8 vs 14x11). This has a tremendous impact on appeal and overall value of the two properties.
Comp #1 was listed for 73 days. Subject property was listed for 2 days and received multiple offers.
While the Appraiser does make adjustments for some of these items, it should be determined these are not like properties and making adjustments does not accurately reflect the value of the subject property.
Suggested Replacement Comps:#1) 215090939
#2) 215065040
#3) 216028328
All suggested comps are 3 bed/1 bath. All are similar square footage. Comp #1/#3 have lake privileges. All comps have garages. None of the comps have full basements. All comps have comparable quality of construction.
Thank you for your attention to the points noted above. I appreciate any considerations you may have in correcting these errors and replacing the comps with properties that are more in line with the subject property.