Comparison properties represent the settings used for a particular comparison.
There are two types of preferences in DeltaWalker - global, application-level preferences and session-specific preferences. The global preferences serve as default values for session preferences at the time a new comparison is created. To change global preferences use the preference pages accessible from Edit > Preferences.... Session properties are accessible via several different ways - File > Comparison Properties..., a comparison's context menu, and selected few are exposed via the main and the local toolbars.
Comparison properties are a subset of the global application preferences that are specific to either a file or a folder comparison. Session properties are overlaid, or applied over, their respective global counterparts. Overlaid preferences is a powerful concept that allows for customization of specific preferences at a session-level, while letting changes to global preferences propagate and affect sessions where they have not been modified.
Let's look at an example:
Say you launched DeltaWalker and you opened a pair of files for comparison. You then decided that you want to turn off the display of character-level differences - you clicked on the dropdown arrow next to the Properties toolbar button and unselected "Show Inline Differences". If the files you're comparing have inline differences you would immediately see the effect of the change.
What you just did was you modified the session-specific preferences for the file comparison you are currently working on. The change is specific to the comparison you are working on and would automatically be saved as part of that session so next time you load it, it will be there. This is not a global-preference change however, which means that if you open a new file comparison it would have "Show Inline Differences" turned on, as this is the default value for that preference.
If, on the other hand, you went and you modified the global "Show Inline Differences" preference the new value will be used in all subsequent new file comparisons. Not only that, but thanks to the overlay approach, this preference will be in effect even when opening previously saved sessions, so long it hasn't been changed it in those sessions. If it has been changed, the session-level preference change would take precedence over the global-level change.