I've been going back and forth with ESRI on my bookmark issues and it has led to BUG-000087557. It seems to boil down to any changes that create a local cache prevent future changes to the bookmark widgets configuration being seen by the user. They're working on a solution but until they do I need to prevent users from doing anything that would create the local cache. In my thinking this would mean the delete button, the add a bookmark button, and, unfortunately, your search functionality. If I can I'd prefer them to be hidden so that I can put them back in the future.