Use solvent that the polymer can dissolve then add in another solvent that the encapsulated agent can partition into.the solvent should be the one that the polymer cannot dissolve
Actually you do not have to 'solubilize' them. Instead, you can use pre-assembled microfilters in microtubes commercially available for example by millipore (trade name microcon). These are microtubes connected by a membrane filter with definite cut-offs and different materials. By this way you can simply filter your final nanodispersion through the filrer under a centrufugal force along with a blank free drug sample with the same concentration.
Technically, a dispersion is routinely filtered, for solutions there are separation methods other than filteration, for example, extraction, reverse osmosis, etc. The final product of the preparation methods in nanotechnology is routinely a liquid nanodispersion which can be simply separated by the filters I specified in my previous answer.