27yr Appraiser here - in 2-4 unit properties, in most markets, rarely is the cost or income approach very relevant (not going to go into the details why). An appraiser is typically going to rely exclusively on the sales comparison approach and hopefully find relatively similar comps to compare the Subject to.
Unfortunately if there are not good comps available (as you stated) you may be more subject to the appraiser's skill and opinions. The proper way to approach this appraisal problem is (summarized below):
* find reasonably similar comps - find relatively recent duplex sales in the Subject's market area and adjust for differences, based on market response (i.e. how much more/less buyers would typically pay for certain characteristics like size of units and lot, location, quality/condition, etc).
* In the absence of similar comps - go back in time to find any similar comps, no matter how long ago and adjust for market trend differences (appreciation, etc), as well as other adjustments as typical (size, bed/bath, condition/quality, location, etc).
* Go to nearby market areas/neighborhoods and find reasonably similar duplex sales and adjust for market area/neighborhood differences as required - along with the other adjustments.
* Find reasonable 3 or 4 unit (not more than 4, and they can use sfr's, but those are typically not as good for comparison. Then they would calculate an estimated market adjustment for # of unit differences. But, generally, this is not very accurate.
Anyway, there are a few more techniques they can use, but this gives you an idea of how they should go about it.
So, as to your specific question, YES, you can most definitely dispute the appraisal if you think there are legitimate reasons to. The best way to do that is understand the different processes I noted above and then to provide reliable, reasonable, credible, and factual information to the appraiser as to why they should consider other factors. Example: providing comp/s which are updated similarly to yours, but may be older sales or in a different neighborhood, and discussing why they should be used. Maybe providing additional info on other comps they used, that may not be readily available. Like contacting the realtors involved in those sales and finding out some pertinent info that caused them to sell below market value. Example: a realtor may tell you the property needed to be rebuilt from ground up due to bad foundation, or ?
Anyway, the basic idea here is you should provide the appraiser a reason to reconsider there value and analysis and just saying "mine is better than those," is not good enough. You also don't want to "shop for value," by cherry picking higher priced sales to justify a higher value. In other words if you have to find older sales or sales outside the neighborhood just because they have higher sales prices, then you are losing credibility. You need a reason and data to support your position that your property is worth more. Your opinion vs mine (as an appraiser) is only worth the data you can provide me to support it.
I hope that is helpful
Good luck
