I would expect the link to come back up when the port comes back up. I looked through some old bug records. Although I did not find an exact match, I saw some bug fixes that could be related. I recommend testing with the latest Intel software as a next step. I would say that you have a fair chance that the issue will be resolved by upgrading.
Download PROWinx64 from http://downloadcenter.intel.com/Detail_Desc.aspx?DwnldID=18725 for the latest version of the drivers and software.