I would leave it alone. It takes time for corals to adjust to new situations, especially after being moved to different tanks and shipping and handling. Dipping works fine for external parasites but I haven't seen anything that shows it has any effect on microbial populations in coral surface mucus layers. Furthermore I seriously doubt any dipping regimen currently being used would only target detrimantal species and leave the beneficial ones alone. Here's some links you might find informative:
"Coral Reefs in the Microbial Seas" This video compliments Rohwer's book of the same title (Paper back is ~$20, Kindle is ~$10), both deal with the conflicting roles of the different types of DOC in reef ecosystems. While there is overlap bewteen his book and the video both have information not covered by the other and together give a broader view of the complex relationships found in reef ecosystems
Changing Seas - Mysterious Microbes
Nitrogen cycling in hte coral holobiont
BActeria and Sponges
Maintenance of Coral Reef Health (refferences at the end)
Optical Feedback Loop in Colorful Coral Bleaching
Richard Ross What's up with phosphate"