Yan,
As far as I know, there is no perfect scale factor for this use-case.
There is a "pseudo-geometry" scale factor, which controls how each pixel on the drawn building model relates to dimensions. If I remember correctly, when you re-set that scale factor, CONTAM will ask if you want to adjust the zone volumes accordingly. But even if that works as expected, making this work properly for your use-case probably would require that you drew the original zone outlines roughly to scale.
If I was going to do this, I would probably just open the PRJ file in a text editor, and update the zone volumes manually. Look for the zone definition section. It will have a header that looks something like this:
-999
14 ! zones:
! Z# f s# c# k# l# relHt Vol T0 P0 name ...
(except the "14" in the second line will show the number of zones in your project).
Then under the "Vol" column, you can adjust all the entries as desired. By the way, if the numbers shown in that column don't match those on the screen when you edit the project, it's because of a unit conversion -- the PRJ always stores things in its preferred units, which I think here will be [m3].
As with any time I manually update a PRJ, I would take a few precautions: (1) save your original file so you don't lose all your work in case you mess something up; and (2) re-open the edited file with CONTAM-W, and spot-check a few of the updated values, to make sure you did things correctly.
-Dave