Because RoboHelp 11 has some enhancements and a new Topic-Sharing workflow (that can be "cloud-based") there have been some modifications. So perhaps it requires a re-connection to SharePoint. Normally, the RoboHelp/Sharepoint integration is most commonly used for source control of those files related to a specific RoboHelp Project. RoboHelp will exclude any "output" files (like those in the !SSL! folder because after all they are output files and not "source" files as source control implies. However, you can modify how this works with some configuration. If you also link to files (which are managed by "Baggage" in the Project Manager); those are added to Source Control as well. (But it sounds like you were already doing that with previous versions, so sorry if I'm stating the obvious.)
I think if would be great if you could take a look at a webinar that Willam van Weelden and I did last Fall. A recording is available for viewing and is free. You can also learn more on Willam's website:
The recording is here (you may be asked to sign in with free Adobe ID)
Willam is more versed in this than I, so perhaps he will chime in with more.
Adobe Certified RoboHelp and Captivate Instructor