I know how to select a section and add palm mutes to the notes but it changes all the notes to the same note. Is there a way to select a section and change all the notes to palm muted notes without changing everything selected to the same note? 

Select note -> Ctrl + M

Oh thank god lol a 16 minute song filled with palm mutes and the guitar pro file had 0 notes marked as palm mutes it was going to take forever thanks a ton smellyorc my wrist thanks you!

You also could have marked the notes in the guitar pro file.

 

You're welcome ;)

Just about every status you can toggle on/off has a keyboard shortcut listed to the side of each function in the "Note>Pro Guitar" and "Note>Rocksmith" menu.

I see that now thanks I never noticed it I always thought the only way to palm mute was to go under pro guitar and edit note.

If the same note is only use as PM in your song, click on the first one, then "select precise like" to select all other same notes in the song, finally toggle the PM status for the whole selection...

I made this on few of my customs to be more efficient...

Thanks Chlipouni that will come in handy too I have had a few songs were that woulda been usable.