Today I downloaded and installed v10.11.4 of OS X (El Capitan). It's the newest version, just came out yesterday to all.
I just tried to open an Inkscape file I had created a few days ago but nothing happened - although Inkscape and Quartz does show as "running".
I decided to try a new download of Inkscape first and "replace" the version I had out there (although the 2 versions are the same) and after I did that, the same file that wouldn't open before, magically appeared..
Now, I'm not sure why but that worked for me. So if anyone else is having the same issue, try re-installing Inkscape and see if that helps..
Good luck !!