All I can say is it's the only editor I've ever used with this type of issue and unfortunately it's a deal breaker for me. I can get by with any other editor even if they aren't my favorite, but only Zed made me realize that the most important thing an editor can do for me is accurately show me files.
Have you checked your fs.inotify.max_user_watches value? Maybe your value is too low and Zed can't watch the files that are changing. I know the JetBrains IDEs need the default to be increased on Linux because they detected it and prompted me to increase it.