Yes it will get overwritten unless you check the 'fix calibration' box in camera calibration screen.
Even unchecked it should help alignment, as it provides a better starting point from which to refine the parameters. it is subsequently overwritten, but hopefully by a more refined distortion model, rather than a worse one.
In short check the 'fix calibration' box if you are completely confident that your imported calibration file is as good as it can be.
*Edit: the above refers only to camera alignment. I'm not sure what happens if you then add GCPs and run an optimization with 'fix calibration' checked. It could be easily tested by checking the 'fix calibration' box, running the optimization and then looking to see if anything changed in the adjusted tab within camera calibration.
**Edit 2: I just tested it. With 'fix calibration' checked you can not optimize any camera distortion coefficients as they are disabled, so they stay the same as when you imported them, but photoscan still modifies the camera positions and orientations to improve the alignment based on your GCP coordinates.