Understanding how to save sessions

Still learning how to do things, but I can't say enough about audition.
One thing that I'm not understanding very well is how to save my sessions with all of the media clips stored with them.
For instance, I produce a bunch of commercials for a client. I save them in one session to keep track of everything. In 3.0, I used to save them with the copies of associated files.
Then, when that client came back with one minor revision, I opened the session, copied the contents of one commercial over in the multitrack timeline (keeping it in the same session) so that I could create that revised copy, and still have the original in the same session.
When it came time to save, I saved it with the associated media files, and it let me save over the previous session, as well as adding the recently added media files to that folder that contained the session.
How do I achieve the same results. I know you can "export" the session, but for a project that is constantly updating, I want to be able to overwrite it and save it with all of the updates so that I'm not creating 30 different sessions for all the updates.
Confusing, i know...but it seemed so simple in 1.5 and 3. Now I'm a little lost.
I tried using the batch save all files, but then any multitrack envelope adjustments were lost after the batch save.
Help!
-Gavan

Here's how I will explain it. I have a bunch of files brought into my session. I edit envelopes on them like this:
Then.... I "Save All Audio As A Batch Process" to consolidate everything in that session into a folder.
But after I run that batch process, this is how the files appear in the session:
It's the same file, just converted. Why is it resetting my envelope points? Is there a way to disable that??
-Gavan

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