All the settings are stored in hidden directories (.kodi, .config, .cache), copying via kodi will probably have missed these - and it's not quite ideal to copy config files while they are being used (eg .kodi folder while kodi is running).
I usually copy filesystems on my linux PC, mount eg both SD card and USB drive and then run `rsync -a ...` as root.
An easier method is probably to use the backup and restore functions in LibreELEC settings. Boot from SD, backup everything eg to an external hdd/flash drive, then switch over to storage on SSD and choose restore.
Stopping kodi and then using rsync (from the system tools addon) or tar to copy the /storage partition would be another method.
so long,
Hias