Thanks Zhang, do you have any idea why would any MUAs mark these emails as deleted? Our users definitely didn't delete these emails as they didn't know about them or couldn't even open them. Our users never use RoundCube or the web-interface to check email, only on their iPhone, Android, Macbook and Outlook.
Even more strange... The same emails were in different folders in RoundCube and SOGo. In RoundCube they were in the inbox and grayed out but in SOGo they were in the Junk folder and not greyed out.
With this specific user in the example and screenshot, the user is using and iPhone and mail app on Macbook to read emails. The configuration on the Macbook is IMAP and Exchange on the iPhone.