Hi,
I get that message *sometimes* in 2012. I found that if I save again, it wants to save the session. I do that, and it saves. I have checked, and all of my new work is there.
It looks like you are coming to 2012 from 2009, that did not have much layers stuff. It was hard to get used to the layers thing, and I don't know that I have done so completely. A couple of basics in case you are not familiar:
As noted in your other thread, you have to be saving a route/session that is yours, or your cloned copy of some other route
I always make sure that I am selecting the session and editing session. Then I go unlock the route once it has loaded. I don't know if this is the only/best way, but so far it works for me as I have modified and merged routes.
Good luck,
Kevin