Asset Server and Dependencies

Has anyone managed to set up a system using the Asset Server in a way where you could have multiple projects updating from smaller "modules"?

Example: You have developed a networking system that you want to use across multiple projects for your team. You make a project with just the networking scripts and objects and dump that onto the server, lets call it "Module--Network". You have another project that is much larger, such as a game, and you want to pull in the network scripts. Using the server, you connect and update from that smaller project, and you now have the networking scripts in your larger project. Lets say someone updates the networking script to add a feature or fix a bug. So you would go to the server, and pull an update down from that project, and your networking is now updated.

The problem I run into is that whenever I do that last update, the local project is now associated with its server version, and the pull from the module forces me to rename the files its trying to replace. It seems like it refuses to overwrite files from other projects, and doesn't give me the option to just replace them, it always routes me to renaming, which breaks every association in the scene.