It's easy enough to make a callback to some JS on the page using the ScriptManager. This code has worked for me inside of an event handler for an event I received through an updatepanel.
ScriptManager.RegisterStartupScript(Me, Me.GetType(), "someKey", "someFunc();", True)
The key isn't as important in this case, but that'll kick off the someFunc JS function on the page. If you can tag a CSS class on the rows that are being updated, you could define a function that does a jQuery highlight effect on those rows. I think that'd be the approach I'd take.
The string there of "someFunc();" gets executed, and the True after it wraps it in proper script tags so you don't have to. I've also used it (for specific purposes) to do things like pop open a new window, like so:
ScriptManager.RegisterStartupScript(Me, Me.GetType(), "viewReport", "window.open('" + reportURL + "','_blank');", True)
That happens in a Button.Click event which lives inside of an updatepanel, so they can click the "View Report" button and it pops it in a separate window, without doing a full page refresh.
Hope this helps or you can find a way to work with it. :)