Note that the original AGI games were designed to be able to run from 360k floppy disks, where each VOL file went on a different disk. Because of this, each resource was carefully put on the right disk to minimise disk-swapping. When AGI Studio rebuilds the VOL files, it does not take any of this into account. This will not be a problem unless you then want to go and run the game off 360k floppies (the rebuilt files will may be too big to fit anyway).
In version 3 games, the resources are not compressed when the VOL files are rebuilt so the game will be a bit bigger if it was previously compressed.
To rebuild the VOL files, select 'Rebuild VOL files' from the 'Resource' menu.