Unfortunately, this problem is still not fixed in the HyperDeck Mini. HyperDeck firmware 7.0 was just released, but it only adds support for the new HyperDeck Extreme 8K and doesn't have any changes for the other HyperDeck models. The most recent firmware that had any changes affecting the HyperDeck Mini was version 6.0 released in June 2018 (which is the firmware version that added H.264 recording in the first place) .
Many video editing programs are able to handle the recordings from the HyperDeck correctly, it's mostly direct upload to video platforms that seems to be an issue.
If you don't want to send the files through a video editor, you can also rewrap the files (without re-encoding the video) using the ffmpeg command mentioned in the middle of this thread:
viewtopic.php?f=4&t=78575