VIRB Edit and Hyperlapse

I'm trying to use VIRB Edit to annotate some video of a canoe trip that I've processed with Microsoft Hyperlapse. The Hyperlapse processing compresses the video drastically, so it no longer matches up with the time scale of my GPX file. I've seen some previous questions regarding this, and typically the answer was to use a VIRB with updated firmware that stores metadata that can inform the application of the time scale. In this situation however the hyperlapse processing strips out the metadata that was recorded by the camera.

I was wondering if anyone has a workflow that allows the hyperlapsed video to be processed. Ideally if I could specify the true length of a video clip in VIRB Edit it would solve the problem, but this doesn't seem likely. I looked in the video files using exiftool and the timescale of my original file was 30000, but after hyperlapsing it was only 600. exiftool can't write a changed timescale, but I'm not even sure if that's the metadata that Virb Edit uses to determine the frame rate of time-lapse video. Other than the time scale problem it looks like VIRB Edit would be the ideal tool for the kind of overlays that I'd like to do.

The video was shot with a Mobius camera. I believe that the same problem would occur if I were to process video from a VIRB camera in hyperlapse (and the hyperlapse app has support for VIRB lens paramters so this is a likely case). The GPX file was recorded by a Garmin Oregon 650, so Garmin hardware was involved in the production :). Some segments (paddling) were shot time lapse, and others (portaging) were shot normal speed. They were all processed by hyperlapsing.