This seems to be a side effect of the workflow for merging audio and video, combined with the fact that HitFilm doesn't span clips correctly.
First off, since Red cameras span ProRes as well as Raw into 4GB segments, long clips are divided into sequences of clips. They're all in a single folder, and the FOLDER should be interpreted as a clip (complete with an included LUT), but they're not so I end up with a bunch of clips for a single take. This spanning thing isn't specific to Red; I've had other cameras do it also like the GH3. The RMD folder + LUT is new to the latest Red bodies though. It's part of the in-camera color grading workflow.
So... I can put them all in the timeline. But merging only works on the first one, and it's broken: the audio is trimmed to the length of the video, and I can't extend it... but merging the 2nd clip SHOULD work, it's the same take, just the next part of it.
Maybe there's a way to combine multiple clips into one, which would be a clumsy workaround for not having a way (that I know of) to import a sequence of clips as a single clip.