This might be an OS issue and not related to After Effects but I thought I would give it a shot here.
I have a project that was created entirely with still images (almost 200,000) shot with a Canon 5D. I converted the CR2 (RAW) to jpegs and edited the project in Final Cut Pro using those jpegs. I then used Automatic Duck to send the FCP project to After Effects where I used the Batch n Replace script from aescripts.com (thanks Lloyd!) to replace the jpegs with the CR2 files for color correction. The problem I'm running into is the script creates a new project where the CR2 files have replaced the jpegs, however everything is offline. The images for each sequence are sorted into folders so I go to the first image in a folder and tell AE to replace it with the proper file. AE thinks for a bit and finds and replaces all of the other images in that folder. Depending on how many images are in a particular folder, it can take anywhere from 5 minutes to several hours for AE to finish. It took over 4 hours for AE to relink a project with 10 shots/images sequences containing over 12,000 images.
All of the AE project files are shared via Dropbox with the other Mac Pro in my studio. I opened one of the projects on the other computer and tried to relink to the CR2 files on my RAID over the network but I had to do each image one by one. Is there a way to relink the files over the network the same way as if they were on my own computer?