Basically, if you set a specific scrolling for only one of the panes this should not influence the other one as shown in the following online demo:
However, I cannot tell you what to do to get the desired result since I do not have your code and there are different setups - e.g external page loaded in a RadPane, dynamic content, nested splitters, etc. and there is not one universal solution for all setups. This being said, in order to let me help the best and the fastest, I would like to ask you to open a new support ticket and send me a sample reproduction demo (a stripped down, fully runnable version of the layout) and some screenshots of the actual and the desired behavior and I will do my best to help.
the Telerik team