I haven't tried this in a while but I thought I lost all my original comping choices when flattening? Maybe I just did it wrong. Never mind, I need to play with this more myself before asking silly questions in a thread about someone else's problem!

Carry on!

Sanderxpander
I haven't tried this in a while but I thought I lost all my original comping choices when flattening? Maybe I just did it wrong. Never mind, I need to play with this more myself before asking silly questions in a thread about someone else's problem!

Carry on!

Nope. Just deslect the Solo button on the flattened comp's lane controls. All your previous clips/editing becoomes audible again.
 
Beware though that the comped lane will play along with the original (which is an exact copy of the unflattened version) so you have to mute it or you'll get the two going at once... and once you start editing the original takes it'll get all wonky for obvious reasons.
 
But yeah... semi sorta off topic.

My vote is for Sander's original suggestion of doing a save as version that's stripped of all of the muted/archived tracks. Having said that, I would definitely defrag first. See if that fixes it. It definitely can't hurt and should be a regular part of your system maintenance if you are using HDD drives. Hint, name your save as something that REALLY tells you that it is not the original. I have done save as "song 1" "song 2" etc. that has left me scratching my head if I leave it go for any length of time