Roundcube is a web-based IMAP email client. IMAP clients do not "download" messages. They allow you to view them in place on the mail server. Because RC doesn't download, there is no way for it to "lose" your messages. If they are gone, some mail process has moved/deleted/downloaded them.
First thing I would check is that the checkbox in the Server settings for "Clear trash on logout" is not checked. But that's not likely to be the issue.
My next question would be to ask if you use any other mail client other than Roundcube to view your mail. In my years as a mail admin, this is by far the most common cause of "missing" messages. If you switch back and forth between Roundcube and Outlook, Thunderbird, Apple Mail, smart phone, etc., the other client may be set to actually download the messages to the client. If that is true, the messages may be visible in the other client, but not in Roundcube (since they have been downloaded and no longer exist on the mail server).