Ha, made it!
Had to do this update from 59.2–>60.4
sudo yunohost app upgrade trilium -u https://github.com/orhtej2/trilium_ynh/tree/node_18_0_60_4 (from here)
and after that just cli update and it worked. Finally!
PS. why if trilium application backup dosent have home folder? When I do manual back, then the home folder is on there.