Im trying to edit midi notes in my tracks, but lots of them have been auto locked and only the pencil tool appears when trying to edit them in PRV.

Are you sure those notes are part of the active clip? PRV will display all notes from all clips in a track unless a) you have the Views menu set up to hide muted notes and b) you have the other CLIPS muted (just the Take Lane Mute button won't do it).
 
Are there clips in the track that are locked? When you flatten a comp it automatically locks the data.
 
Just some things to look at.

And in case you weren't aware a locked clip will have a little padlock symbol at the top left of the clip. Right Click and select Clip Lock and deselect Pos and or Data to unlock it. This can also be done in the Clip Inspector (Press I > click Clips Tab at top of Inspector and look for the Lock Pos/Data section).
 

Beepster
And in case you weren't aware a locked clip will have a little padlock symbol at the top left of the clip 

 
Oh no that's a BIG icon. I even submitted a feature request to make it smaller. My Track view is full of big padlocks!
 
@OP: Hit Ctrl+A and then Ctrl+K. This will unlock all clips.

Yea they werent locked with the padlock, just couldnt edit any notes.
 
Selecting the track individually and then going into PRV fixed it, I was trying to edit in PRV without selecting the right part of the track.