flatpak steam keeps save files in:
/home/$user/.var/app/com.valvesoftware.Steam/.config/unity3d/Eleventh Hour Games/Last Epoch/
“normal” steam keeps saves in:
/home/$user/.config/unity3d/Eleventh Hour Games/Last Epoch/
After reinstalling steam flatpak, installing normal steam, and then back to flatpak i lost my character. On 2nd time of installing flatpak steam “decided” to keep saves in “normal steam” directory,
so i had to copy them to new dir, everythings works now.
Maybe someone will find is usefull.