Hi,
You can export the texture as tiff and work on it in Photoshop, the great thing is you dont need to use all origin photos for texture creation, and you can choose the ones you are focussing on. Layer them in Photoshop, repair and import again to Agisoft. The other way is creation of UV map (ZBrush or similar), working on the texture directly in Mudbox (similar tools like Photoshop), thats the best way to do it, as you under control of your texture map projected on the final mesh.
Good luck, regards, Andreas from fabberlounge