C: A0006 UID STORE 1:* +FLAGS.SILENT (\Deleted)
This is a command send to the server. It marks messages as deleted. I don't see a response from the server, it means it just take too long and most likely connection time limit makes abort. In that case Roundcube displays error and refreshes the messages listing.
The messages are marked with gray color because they have been marked on the server as Deleted.
As you see it is a "slow server" issue and I don't think we can do anything about it.