The Control Panel was never designed to be themed, so you will almost certainly have problems on any upgrade of CS. Where possible, I'd suggest you keep theme changes made to the control panel to within the stylesheet as your stylesheet should still work in future versions of the CS Control Panel.
If you did base your custom theme on Calypso or lean and green, you don't have to scrap the themes - you can keep all of the styles, and the majority of your work will still work - Typical changes you may need to make are chainging CSControl:... to CSForum:..., CSBlog:... depending on the context in which the control is being used. If you're still stuck on the markup change you need to make, have a look at teh equilivent page in the default Hawaii theme and that should put you along the right lines.