Well I would guess on the next upgrade you could modify the Install package to exclude core modules that you have made changes to thus far. The only drawback to this method is that you might not get the new functionality/bug fixes/enhancements associated with the latest core module releases.  My practice has simply been to keep notes of the changes I've made to ccs  files associated with core modules and to rename them before my upgrades.  Once the upgrade is complete, I go back and delete the new ccs files and rename my previous one. Before deleting,  I would compare any new css file with the previous ones as it may contain new classes/selectors that define the newer release.  You also have to be aware of modules that come with pre-defined templates or themes you may have made modifications to, such as the repository module.  There may be bettter ways of doing this so others may chime in and I can learn something to.

Paul

I typically just save copies of my CSS files before an upgrade in a seperate name. Once the update is complete I pull both CSS files into a text compare software and have it mix and match for me. Thusly I get my changes back, while allowing for new CSS classes / styles to exsist. Then I typically go back and run through the new CSS file to check for any new classes I need to change to match my current theme. Nothing like setting text to orange just to have a weird class change part of it to green.