At any time working on a project in SizeIM, you can go back to your Master Layouts to make changes. Clicking on the Generate button on the main SizeIM Toolbar will then apply these changes to your Ad Sizes.
If it is the case that you wish to exclude some sizes from the regeneration, open the Ad Settings panel by clicking the cog icon for the Ad Size you wish to exclude. In this panel, check the ‘Ignore Regeneration’ checkbox. You can then safely regenerate without affecting that Ad Size.