Always keep a backup of your save data. Never delete a copy of your save data unless you have made sure another viable copy exists.

Dark Souls II handles save data in the same way as Dark Souls III, so this guide will be applicable with only a few minor changes: https://gtm.steamproxy.vip/sharedfiles/filedetails/?id=961512800
Here's the changes that make the guide applicable to Dark Souls II:

• Save folders will be stored in the DarkSoulsII folder instead of DarkSoulsIII.
  
• Save data inside save folders will be called DS2SOFS0000.sl2 instead of DS30000.sl2.
  
• The linux file path includes the app ID of the game, which will be 335300 instead of 374320.