Hi,
If you have touched the "PHP" files, then i am afraid those changes will be gone, because you have to override the PHP file by installing the new CleanMart... If your changes are only about "styling" and if you only customized the "flexible.css" file, then you can use your old flexible.css file in the newest CleanMart version. So; your styling changes will be preserved.
But i would strongly suggest you to test everything in the localhost. Create 2 sites;
1- With old CleanMArt and old Virtuemart,
2- With new cleanmart and new Virtuemart..
Then carry the "flexible.css" file to from 1 to 2 and see how things look like in the front-end; check if your customizations are carried. If you have touched the PHP files, then you can carry those PHP files as well. But do the migration one-by one; so if anything goes wrong; you would be sure what breaks things.
Regards.