I figured out how it worked for me maybe it will help you too.
1. Go in the \Steam\steamapps\common\ATLAS\ShooterGame\Binaries\Win64\BattlEye folder and doubleclick the Uninstall_BattleEye.bat
2. Delete everything in the BattleEye folder
3. Go to steam rightclick on atlas properties / Local data and let it check for errors/missing files
4. Start atlas and login to a freeport server and kill yourself and spawn in your bed
Hope it works for you too