Hi A. Malcolm Campbell , do you know which type of oil you plan to use? With organic oils people tend to do a series of washing steps with a low viscosity organic without surfactant (e.g hexane). For fluorocarbon based oils you can use a detergent such as perfluorooctanol to help destabilize the emulsions and then collect the aqueous phase directly. The fluorocarbons are a bit easier to work with if you have more sensitive products in the emulsions.

Thanks Joseph. I am not sure yet. We have not started so we want to choose the best oil. Am I naive to think that simply spin to combine the droplets and then pipetting aqueous phase? We want to pool droplets with shared properties so we can do PCR on the contained DNA. If not, sounds like fluorocarbon-based oils are best bet.

Spinning can work it just might not be very efficient if there is surfactant stabilizing the droplets.

In the microfluidics field fluorocarbon-based oils have become pretty standard for biological work. It tends to be more biocompatible and easier to work with (although more expensive). FC40 and HFE7500 are the most common oils and biocompatible surfactants are commercially available from RAN, Spherefluidics, among others. Prior to this Mineral oil + Span 80 was also very commonly used.

This review is a bit old but could be helpful https://pubs.rsc.org/en/content/articlehtml/2012/lc/c1lc20582j