Presuming you are refering to QlikView server.... there were certainly issues with doing an over the top install with the first release of QV9. I am not aware of these being addressed with the two service releases - but they may have been.
The reccomendation certainly was that you should comletely uninstall QV 8.5, including removing registry entries etc.. The downside of this is that your reload schedules will be lost and will need to be re-applied under version 9.
QlikView documents created in v8.5 can be distributed with server v9 without any changes being required to them.