I can actually now repeat the problem on demand. If you would like to test it for yourself set up a test sequence with some random clips. Three or four indvidial clips will be enough. Now nest those items and save the sequence - call it "Buggering Test Nest 01."
God - you can tell I'm procastinating can't you (must be on deadline or something).
Now create a second sequence then copy and paste Buggering Test Nest 01 into it. If you prefer you can drag the nest into a bin and then drag it to the timeline (it doesn't matter).
Now say loudly "well I don't like the way these clips are nested I shall delete the sods." Then double click on the nest (which will open the nest as its own sequnce timeline) and delete the clips. Close the now empty nest sequence and look at the new/second sequence we created. You will see the thin strip of remaining empty nest.
Now here is the fiendishly clever part. Accidentally on purpose press shift and delete at the same time ('cos we're human and all make mistakes - except for really snooty gits who are untrustworthy anyway) . The empty nest is deleted. Now try and save the project. Chances are you won't be able to - no matter what you do.
Oh and it also disables the autosave feature - I tell ya it's the work of the devil.
if you can save it - you obviously haven't effed it up properly.
My point all along has been to advise other users who run into this fairly rare but deadly situation is that there is nothing you can do - and don't do as I did - spend hours trying to figure out a workaround when there isn't one to be had. Just bite the bullet, quit and restart. Then cry as you re-do all the work you lost.
I have heard mumblings about maybe finding a slightly more recent saved version in the autosave vault... in the interest of full disclosure I have not tried that.
There are those who say - "well pros don't make mistakes..." My advice is to flee from such people quickly as they are probably verging on the sociopathic." I learned that tip from working with Nic Roeg many years ago. Fabulous mistakes often lead to incredible work - though more often than not to a bucket of poo.