I was just playing around with a JumpList in WPA app. I have added this code to my App.xaml:
<JumpList.JumpList>
    <JumpList ShowRecentCategory="False" ShowFrequentCategory="False">
        <JumpTask Title="New Note" Description="Create new note"
                  Arguments="/new" CustomCategory="Actions"/>
    </JumpList>  
</JumpList.JumpList>
Then i decided not to include that functionality in my app, so i removed those lines of code, but the item is still on the JumpList when i right click the taskbar icon.
I found solution that points to delete files from %APPDATA%\Microsoft\Windows\Recent\AutomaticDestinations\, but it didn't help.
Cleaning or rebuilding project didn't help.
                        
As discussed in the comments, you need to leave an empty
<JumpList>in your application and run it once. You should then be able to remove the<JumpList>from your markup completely if required.If the
<JumpList>element isn't present, the code to update the jump list never executes, and Windows continues to use the previous jump list.