I’m using confluence and Emminence 2.0 skin.
I’ve not experienced disappearing addon shortcut icons.
Your log shows this:
Mar 04 16:00:22 osmc kernel: VFS: Mounted root (ext4 filesystem) readonly on device 8:2.
For some reason the root filesystem on that system is read only.
I’d sudo fsck /dev/sda2 and reboot.