There are times when ReSharper gets confused. It might be unable to locate references if you've been re-jigging your packages (oo-er) or it might be unable to perform a refactoring on a file because its in read-only mode for no good reason.
While there's always ReSharper clear caches through the Visual Studio settings...
I've been using the command line more recently, so decided to make a script to do this from the root directory of the repo. Depends on having Git installed on the command line. And expects the ReSharper version is 8.2. And that you haven't tweaked where RS keeps it caches.
Its a PowerShell script, so add the contents to your PowerShell profile and set an alias if you like.