Here are a few tips on things that I have done to control this appraisal issue and mitigate the risk of low appraisals:
1. Try and find a lender that is familiar with FHA flips and has a pool of appraisers they normally use. The lenders I work with usually have 5 - 7 that are on their "list". Then have your agent have a letter on file that the seller requests buyers get pre-approved with your preferred lender. Some agents might get annoyed by that, but if you sell them on the idea of a quick closing and few issues they will usually play ball. The benefit would be using trusted appraisers who understand the lender's business and can come in with the necessary value.
2. If you are close to having seasoned the property for 90 days and an offer comes in, you can accept the offer and then rewrite it on the 91st day (make sure everyone is on board with this and understands why). Then the lender can order the appraisal and create the FHA case number and the 2nd appraisal should not be required. You may lose a few days, but well worth it.
3. Others have mentioned it, but meet the 2nd appraiser and tell them they are the 2nd appraiser and hand them the 1st appraisers report. Often times when its a query system that is being used to order the appraisals they don't even know they are doing a 2nd appraisal, they just see the order and do their job. Make it easy for them.
4. If one of the appraisals comes in low, ALWAYS ask for a reconsideration of value and TELL THEM how much you need. If its a few thousand it should be a piece of cake. I actually just got an extra $16,000 on an appraisal today. I emailed the appraiser, thanked him for his work and asked what he thought of the attached comps because I was $15,000 away from what I needed. In one day he revised the appraisal and sent it to the lender. May not always work, but might as well ask!