In order to keep KF2's data safe, including perk levels, you have to enable cloud saves prior to data loss. This is done manually:
https://www.epicgames.com/help/en-U...-cloud-saves-in-the-epic-games-launcher-a3600
If Epic Games promt you to recover data from local saves (files that are stored on your computer) do not use those, they could be corrupt or empty. Situations such as power outages or sudden disconnects from the internet are known to corrupt local saves.