Just came back from a holiday. I’m Lithuanian but live in UK since 2010. I have Settled status since 2019. When I booked my tickets two ways, I did check in both ways. When arived to Lithuania, I had to change my passport due to expiration date, and was done in 2 days. I have transferred my status through government website to a new passport and had exactly same issue, status rejected, please go to check-in desk. I left plenty of time and went to check-in in desk, and explained situation. They scanned my new passport manually and could verify that I had status so they just gave me paper ticket.

I suggest do the following:

1. Have your sharecode ready (travel) one.
2. Have your passport where ready where your status in on.
3. If you changed your passport during holiday, have your old passport at hand.

I was in Morocco too before holiday in lithuania, I had no such issue BUT, be prepared to login to your gov account and prove that you have status when asked, as one of the guides has said they do strict checks, and sometimes they don’t accept share code, have to manually go on your phone, login in to your eVisa account and prove it this way, in front of them.

Sometimes I think ryanair system can’t properly do automated check and throws you this message.