I believe you need to do what is called, "Pack and Go." To my understanding, it takes all related files to an assembly and the assembly itself and places it into one file that you can open up on any computer with compatible software without having issues with file linking.
Our team had quite the experience with this issue uploading our Inventor submission last year. We tested our submission and found that every file link of the over 5000 parts on our robot CAD was not working. We read up about a solution and pack and go came up. It was actually very useful!
Here is an explanation and quick tutorial on how it works.
Disclaimer: This might or might not be what you are looking for.