I should write up some documentation on the storage options. I recommend that flatfile is only used on test servers, as it only saves clans when the server cleanly exits. Not when it crashes (even if the crash is not MCClans related like yours).
If the server has been running for a while there should be some backups generated in
config\nl.riebie.mcclans\data\backup. There's two things you should do. Switch to the mysql storage option, and restore one of the backups.
Before you start find a backup that has saved clans. In the backup folder start with the most recent one and look in the
clans.json if there are any clans. If so, copy the four
.json files to to a save location, we'll need it later (in step 3). If there are no clans in it, look in the previous backup and so on.
Switch to mysql and restore the backup:
1) Stop your server.
2) Go to the config and configure the database section.
3) Copy the four json files to data/load. What this does is trigger MCClans to load the data from these files even though it is configured to use a database.
4) Start your server, and check the logs for warnings to see if the database is configured correctly. If it's not, repeat from step 1. If it is, your files from step 3 will be loaded in and converted to the database.
If you need any assistance with this let me know and I can help more directly through discord / teamspeak / skype / etc.