Sorry, TheHumanCreeper, your original post slipped past.
Are either of you running Universe Sandbox ² on both Mac and Windows machines? We've encountered an issue when sims are saved on a Mac then moved to a Windows folder, causing all sims to disappear in the Open menu. We have a fix for this coming in the next update.
If this isn't the case, would you mind either emailing us your saved sim files, or attaching them to a post here? You can email them to support at universesandbox.com.
Thanks!