I can chime in here… there’s nothing wrong with Cubase. This is a bug (or rather, poor implementation) on Liine’s part. Their virtual MIDI ports don’t get reassigned the same CoreMIDI unique ID (which they should, as outlined in Apple’s CoreMIDI documentation) so even though they have the same “name,” every time you reboot or quit/relaunch the Lemur Daemon, Cubase sees all new MIDI ports.
How do I know this? I actually coded my own daemon app to circumvent this issue (plus many others) after researching the issue. (EDIT: But there’s a workaround I posted two posts below)
You can try submitting a bug report to Liine but Lemur is almost looking like abandonware these days. There has been almost no interest shown by the developers in over 2 years to maintain the product, fix bugs, or introduce new features.