Hi Luftz,
A thing you can do is to export your detailed mesh at the lowest subdiv level to maya. Fix the bad polys. Export the model back to zbrush, and append it as a new subtool for your detailed zbrush model.
Then you divide your new corrected model, so it has about the same amount of polys as your detailed model.
Then it would be a good idea to make a morph target of your corrected model, so if there occures any projection errors, you can fix it with the morph brush or the smooth brush.
With only those 2 models visible, and the new corrected model selected, press the ‘projectAll’ button under the subtool palete.
And woila, you have projected all your hard work over to a clean mesh 