I don’t think there’s a command line option to collect files, and there’s no scripting interface for Collect Files, either.
There are two options I can think of that are close to what you want to do if you’re willing to do some scripting.
1. Write your own “collect files” logic in a script (identify assets, copy them to a location, reconnect each item to the new footage location), and call it from a separate instance of AfterFX.exe from the command line.
2. Save your AEPs as XML, and write a script or tool to parse the AEPX file for paths, copy files to new location, and update the XML with the new paths.