I forgot to set my camera (GoPro) to inverted mode and now have an entire time lapse sequence upside down.

I tried using the image transform - rotate to fix the keyframe photos, but it doesn't seem to have saved this information out with the XMP metadata?

Is there a trick to rotating images for LRTimelapse?

Just rotate them in Lightroom before exporting the video like you did. It doesn't matter that they are not rotated in LRTimelapse...