I'm sad zzTakeoff had no workflow for us, and we are left to fend for ourselves. Right now I need to make many projects to have the outcome of tracking changes of estimates. Any ideas here besides making so many projects?
We are forced to use file names, which will never scale. Example below:

We'll get there. Bryan K has dealt with this via a layer per plan set accompanied by putting all plan files in an accompanying folder. Details near the bottom of this post. Eventually we will build a cleaner way to isolate multiple project takeoffs into buckets (kind of like layers that have their own set of plans). This may be a matter of just improving how our software handles plan versioning.
Autodesk Takeoff (now Forma Takeoff) had a neat way of organizing this. I believe they called them 'Project Snapshots' or something similar.
I think the revision system is heading in the right direction. A couple things that are missing:
SD/DD/CD sets are so drastically different coming from a GC...... I feel like what I've seen here mostly deal with addendums and minor changes from all you detail trade partner nerds that only see completed sets.
One idea I have in order to contain this in one project as you have it, is to make a major, MAJOR filter at the top shown in my sexy UX blue text design.
This would filter out all drawings, measurements, items, anything related to old reports from every other milestone plan set before it.
Try searching the PDFs......boom only the current milestone set SCORE!
Try running a report..... sweet no crap in there from old SD drawings wahoo!
Try sending this to estimating software....... sweet it didn't send any of the old crap, wahoo!
Look at the layer dropdown......Sweet its a new fresh dropdown not have the old crap!
