I found a work around. I installed mkvtoolnix and then opened the mkvmerge GUI and opened the file and in the video, changed the FPS to 30 fps and then "merged" it to a new file. After that VRD TV Suite could open and save it without issue. I didn't try re-encoding, but I didn't need to as the audio wasn't messed up when doing smart re-encoding. mkvtoolnix is a bunch of command line tools with some GUI wrappers, so it could be run from kmttg if need be.