I was having some issues with modifying a huge project of mine and noticed some key things that would improve troubleshooting:
1) Timestamps on Undo/Redos
This would be useful if you knew the time it last worked.
Highlighting the lines that have been changed, and the ability for the software to focus on that specific change would also be a great boon as you can tell what has been changed.
Currently without that, it's a crapshoot because if you need to undo a lot, you don't know what you're undoing.
There are also more things they could use as well, but those two are the only ones I can remember atm.