If audio files are created, then deleted from the track view, they will still be in the audio folder until "clean audio folder" is run (or they are removed manually).
 
So.. wouldn't the project sample rate be fixed to that of the rendered files?
That would make a sample rate mis-match the likely cause of OP's problem.

My son had a weird tempo issue on playback with one project, and it turned out to be some kind of issue with groove clips or something like that - sorry my memory is bad on this, but it was a couple of years ago (4? - yikes).
 
I am hoping the above may trigger someone's knowledge/expertise on what might be underneath these issues.
 
All I can remember about the situation was one of the Bakers noticing some kind of tiny indicator about the clips. that then told them what was going on, and then when my son undid whatever it was that made that little indicator show up, the issue instantly went away.
 
I again am VERY sorry these days I am a bear of very little brain - the passage of time and the foggy effects from the meds for my chronic pain have robbed my of better memory of the situation and solution.
 
Bob Bone

Good to see you still around Bob. 

Thanks, Cactus, hope you and any little cacti are well.
 
I never left - never contemplated leaving.  I have been dealing with some musical preparations for a Genesis tribute project based in the Chicago area - so have been off brushing up on my playing the more epic Tony Banks solos, of late. 
 
The WEIRD thing about it all is that some of the absolutely most simplest sounding parts of some of the songs are actually chock full of sneaky meter changes - like sometimes literally every single or every other measure.  The quiet section in the middle of Deep in the Motherlode is a constantly shifting bunch of meter changes 4/4, 5/4, 6/4, but all played over a quarter-note based bass note, so you wouldn't really notice unless you were trying to play the changes.
 
Anyways - thanks again - I wish my earlier post for this thread would have been of more help.  I just cannot recall the details of why my son's project suffered such a mysterious slow down, or what fixed it.  I was hoping to jar someone's memory - since my memory is quite full of holes these days.
 
Bob Bone