- Don't use EPS with InDesign!
- In the link panel in the flyout menu are menu commands to relink files with a different folder or with a different extension.
Relink to folder / Relink to Extension
I wrote a script for this task: Restore broken links after server migration in InDesign.
The main idea is replace the part of the links' path which is different assuming that the remaining folder structure is the same.
Warning: some people report me that the script works for them, some that it doesn’t. I can’t solve the problem without debugging the script on a computer where it doesn’t work.
The best way to deal with this is to keep the path as short as possible. I realize it helps keep things organized to have a deeper folder structure, but if all the images were in a single folder, you'd only have to manually relink one and InDesign would find the rest on its own.