It is difficult to be selective with many difunctional compounds.
The major issue you will face is the inevitable reaction of the remaining acid group with the acid chloride formed. If the molecule allows intramolecular cyclysation, then this will be a dominant bi-product. If the molecule does not favour cyclysation then you will form an unstable acid anhydride polymer as one of your products.
You need to consider an alternative route, such as replacing one of the acids with, for example, an aldehyde which can be oxidised after you have reacted your acid chloride
All of this is dependent on your molecule and what your ultimate target molecule is.