Check out the following two threads. They have the two flight paths that got the name changed and how to fix them. Just replace the file name with the reputation one for alliance and search for any mention of the flight paths for getting them changed. I think it will be the Moa'ki Harbor name change that's in the 2nd link.
http://www.zygorguides.com/forum/sho...st-guide-error
http://www.zygorguides.com/forum/sho...ievement-error
http://www.zygorguides.com/forum/sho...st-guide-error
http://www.zygorguides.com/forum/sho...ievement-error
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