Recommended software/techniques for filling in incomplete Freestyle lines

I’m working on a project that uses Freestyle and have found that Freestyle is somewhat inconsistent as far as outlining things. Worse, since I’m working in stereoscopic 3D, sometimes a Freestyle line will be rendered in one eye but not in the other (see here).

As far as I can tell, there’s not much you can do about this, so it looks like I’m going to have to perform a manual post-processing step to draw the missing lines. This also applies to drawing missing lines in, say, only the left eye frame because the same lines were successfully rendered in the right eye frame.

Any suggestions on how to best go about this?