Whilst you can use RoboHelp Server to host your online output, it is not a colaboration tool. If you are getting issues with missing files inside your source control application, please provide some further detail and we'll try and help. There should be no reason why either RSC or TFS should report missing files.
I'm going to differ from Colum a bit and say that RoboHelp Server *CAN* be used as a collaboration tool if you use it in a specific way. Just as there is more than one way to "skin a cat", there is more than one way of collaborating.
One way of working would be to split your projects up so that each author becomes captain of their own ship. By that, I mean each author maintains sole responsibility for editing one or more specific projects. Because nobody has their fingers in each other's pies, there is no source control needed or involved. When finished, each author generates a "Pro" output and publishes to the RoboHelp Server. The RoboHelp Server handles presenting the collection of projects to the users as if it were a single project by performing a merging of the Table of Contents, Index and other items.
Whether or not this sounds like an avenue you wish to pursue is totally up to you. I'm simply making you aware it exists.
Helpful and Handy Links