Agreed that Cycliq's tech support is great, I'd reach out to them.
That being said, some things to look for is to make sure you don't have locked files on the SD card. If it gets to a point where it fills up and can't overwrite the files, that's definitely going to cause problems. If you have the new Fly6 CE you can have it reformat the SD card from the App. If you have the older v2 you can tell it to re-format the SD card in the config file. I ran into a similar issue with my v2 and having the device reformat the SD card instead of doing it myself on my computer resolved the issue.