When the plugin loads, it should load that skills file into memory (if it exists), and then on save (which happens on unload) it will save the skills that are in memory back to that data file. At some point, it either must not have been able to save that file properly, or it was not able to load the file properly. In the config, you can try setting "SaveOnServerSave" to true, this will save the data file every time your server does its routine save. However, I only recommend doing that if your server is configured to save infrequently, like every hour or so. If its saves every minute you will get lag if that is set to true.
I recommend trying this out. Please do keep me updated if you come across this issue again OR if you see any error that occurs when the plugin is loaded/unloaded.
You can also use the "/qc playerdata backup" command to create a copy of current player data. The plugin only keeps one backup at a time though, so after you create it I recommend renaming the backup file or copying it to a different location so that you can restore it later.
I hope this gives you some options to work with.