If you are marking up a website, the first thing you'll want to do is check the other device views for your MarkUp. When you click a link to view a MarkUp comment, it will take you to the default desktop view. If the comment was left on the tablet or mobile view, you will need to navigate into that view to see the comment. You can quickly see how many comments are available within each device view by clicking the device icon towards the bottom of your MarkUp.
You might also lose your pins/comments if the website changes the content that you previously marked up. If you are commenting on a site that gets regular updates, you might want to save a PDF version of your website to mark up so you can ensure your pins stay in place as long as you need them to.
Another reason you might have lost your pins/comments could be missing is if you are marking up a website with a malformed canonical URL. If your website was coded with a dynamic canonical URL or it simply wasn't coded right, you could experience an issue with your pins/comments disappearing. If you are able to ensure your website has a properly formatted canonical URL without any dynamic parts to it, that will ensure your pins/comments stay in place. If you are not able to alter your site's canonical URL, you can save a PDF version of your website and mark up that version instead to ensure everything stays in place.