Self-referential aliases in referenced files

I migrated my photo library from iPhoto to Aperture this week and created a referenced library that manages the first 40Gb of my 200 Gb of images on a Network Attached Storage device. The migration copied the images from a local copy of the library to the server. All of the images seem to have migrated, and when I view them through the server's file browser (which is running Synology DSM 3.1, a Linux based file system using EXT4 formatted disks) I am able to download the files and work with them. However, Finder believes that some of the images are aliases rather than actual images. The impropperly aliased images are all in the same folder. When I view these files through a mounted drive by selecting "Open in Finder" within Aperture (or navigating to them through the folder structure in Finder) the client believes that the server contains an unresolved alias, and offers to do me the kindness of deleting it or redirecting to another location.

When I open the info view of the file which Finder thinks is an alias, it shows two paths that are very similar. For example:

Where: /Volumes/Share/Container/Aperture/

Server: afp://192.168.0.190/Share/Container/Aperture/

Wherever this aliasing behavior came from, it predates Aperture's interaction with the file. I know this because I checked backups of the iPhoto library and found the aliases to already be in place. This is only happening in a few folders, maybe 5% of them or less. The real question is this: what is the best way to replace these self-referential aliased files with the actual files?

(I edited my original message once i found that the problem predated Aperture import)