If you want to keep your scheduled tasks, you can backup the C:\ProgramData\QlikTech\ManagementService\QVPR folder and its contents, and restore this folder after you reinstalled or fixed your QlikView set-up.
However, problems with documents and tasks are often caused by renaming documents that have still tasks attached and such. So I do not really know whether this is the way to go.
Do you have a complex task list? Many mounted folders? What version of QVS are you using?
I have seen this behaviour in QV11 SR2, but it was only random occasions and a browser refresh normally fixed it. Is this the same for you? When it happens, do you also lose folder structure when viewing the server documents via Qlikview desktop? I've only seen it happen via the browser.
I also recall it was only mounted folders affected for me.