That button shows you which topics from the current category you have bookmarked. If you are within a particular category and go to that button, then you only see what you have bookmarked within that specific category. This is important as it would not show all your bookmarks in that case.
Having said that, if you are at the homepage, then the /bookmarks may get all your bookmarks since you are the top level of all categories. For a proper full list of your bookmarks, you can find on your account.
Indeed, after updating to Discourse 3.1 there were issues with disappearing bookmarks which we have reported to the Discourse team. And today we have updated the forum to the latest Discourse version so it’s likely that it includes the fix for this.