Cotton and Norman exchanged trifluoroacetate for acetate using trifluoroacetic acid and trifluoroacetic anhydride. This might serve as a model for what you are trying to do.

Article Molybdenum(ii) trifluoroacetate dimer

Alternatively, you could make the potassium octachloromolybdate from the acetate, then use the silver salt of the new acetate to effect metathesis.

Thanks for the clue Prof. Hanson

If you aim to insert your acetates you should just start from another molibdenum salt, choosing it's anion and the counter ion of the acetate so that one of the two products will precipitate while the other remains in solution (playing with solvents may also be usefull). To switch acetates with labelled ones will always result in a not perfecly pure product, but in a mixture of labelled and not.

It is nearly impossible to 100% substitute the carboxylates using an acid and anhydride. The lack of complete substitution resulted in many problems in assigning the spectra and substitution chemistry. The best way is to synthesize (NH4)4Mo2Cl8. This compound is slightly soluble in alcohols and the chlorine atoms can then readily be completely replaced by any carboxylate by just reacting this with the appropriate acid.