I don't use the "safety net".
But in very simple terms (I'm a simple-minded guy), I believe this is how it works:
Source drive has files:
file a
file b
file c
You run the first CCC clone.
Backup drive has files:
file a
file b
file c
Now, two different scenarios:
Scenario first:
You delete file b from the source drive.
You run an incremental cloned backup with safety net OFF
Backup drive now has files:
file a
file c
(Because that's all the source drive has on it, since you deleted file b)
Scenario second:
You delete file b from the source drive
You run an incremental cloned backup with safety net ON
Backup drive now has files:
file a
file c
(in a special folder -- I forget what this is named):
file b
Thus, even though file b is no longer on the source drive, CCC has segregated and preserved it in a special folder so the file is not automatically deleted.
I believe this will work with "changed" files as well.
If safety net is on, and you changed/edited a file, both versions will end up in the backup.
The "current" (changed) version will be a part of the "regular clone".
The "old" version will end up in the "preserved items" folder.