I just added collision-protect to make.conf and got this error when updating world. I don't know if the problem lies in portage collision detection or if it is the package's fault. Strange things is that the two files are actually symlinks (see details below). Equery reveal the files belong to foomatic-filters (the currently installed version, but I don't know how it handles symlinks.
Created attachment 102575 [details] emerge --info output
Created attachment 102576 [details] error message from emerge
Created attachment 102577 [details] ls -la output of conflicting files
*** This bug has been marked as a duplicate of 16162 ***
*** Bug 155988 has been marked as a duplicate of this bug. ***
*** Bug 156058 has been marked as a duplicate of this bug. ***