Most of it was fine, but my editor had suggested a rearrangement of the back-story that's revealed in flashbacks and diary entries. Man, this was difficult! The manuscript is 300+ pages long in Word and various scenes needed shifting around, sometimes by a significant number of pages. My editor had very kindly provided a 'new running order' (which was even colour coded!) but had suggested that the back-story could be stretched out even further. I could see a few extra changes, but even with her running order and my notes on where to move things, I was getting totally lost at times. So yes, I resorted to good old Post-It notes and maps and time-lines to try and keep me straight! I suspect my husband believes we will never end up using our dining room table for its original purpose - it is forever covered in Post-It notes or index cards or print-outs of whatever I'm working on, not least because it's a decent sized horizontal surface (which also extends if needed!).
Anyway, the edits are now just about done and ready to send back, so that my editor can go over it (and make sure I've not totally messed it all up!) while I'm on jury duty.
How does everyone else keep track of these kind of changes?