Are you talking about individual files or projects? I assume individual files, since 49,000 projects may be a bit on the heavy side.
If you add a project to version control, RoboHelp will add all the files to SharePoint. This will take quite a bit of time (set RH to add it before you go out for lunch or before you go home). In the end, you can check in the entire project with a single click. Or are you seeing something else?
You can always manipulate RH's .apj files to very quickly add loads of files to a project. If you have the files in SharePoint, you can update the FPJ files (Use the following script: Missing topics fixer). Then remove the CPD and start the project.
Yes, it was files, about 15 projects, but now I have to get RoboHelp to connect to SharePoint, and that's something I haven't figured out. Everything is nicely in SharePoint, but it's one error message after another trying to get RoboHelp to allow version control. I can open SharePoint files within RoboHelp, but I can't get the versioning to work.