hello,
perhaps i can try to help you my friend, what is the solvent used in the oxidation? the allelic compound, what it is like? do u mind giving a picture so i can have a idea of where the oxidation would stop?
depending on your conditions, u can filter off, and remove the AcOH in the rota evaporator, instead of extracting, u might be losing your compounds there. If u have a ACID as product u HAVE to use acid for the extraction. If u use base u will most likely have it hydrolysed.
hope i can help