The quickest way to fix your messed up photo locations is reload a previous save.
If you however live in the real world where you don't save every second, you might have to realign the entire dataset.
However! In the Reference tab you can also uncheck all your GCP's and check all your camera's and "Optimize Camera's". This might return your camera's to their original location.
At work I also have the delight to work with 2 coordinate systems. After some searching i found that you can tell Photoscan to ignore the coordinates the camera's have and just use the GCP's. To achieve this go to the Reference pane, and disable all the camera's. Then enable all your GCP's and Optimize your camera's. This works for me.
Hope it helps you a bit.