Yes, in new OJS version the way how file uploads are managed has changed. This includes changes you described as well.
Only those that are editable or automatic reminders/notifications also? Can you describe a case in more detail and I’ll try to help you with debugging?
In general, they should be writable by your web server (usually Apache). Exact permissions depend on system configurations: How should file permissions be set? - #2 by ctgraham. It’s also important that files dir is not web-accessible