Running 6.2.3 on a farm using the Content Resource Management.

When site is built from template, I log in to the site, check the override host settings checkbox and click update.

I make whatever changes I need to the portal.css, and save it.

I go back into Site Management and uncheck the override host settings checkbox and click update.

Most times when I do this, everything works. Occasionally, when the box is unchecked and updated, the site reverts back to the previous css.

If I clear the cache, it will display properly until I log out, then it reverts to the old css. The only surefire fix I have found is to delete the actual .cdC file out of App_Data/ClientDependency. 

I have 60 different skin templates that will be used for over 3000 portals. I need to be able to make changes to each one and have it reflected with the css and js minified in composite files. Even if I override, check the options to use composite, and minify, it still does not reflect my changes; even after incrementing the site version.

Basically, something is wrong with the system, and I need to know how to fix it, or if DNN is planning on fixing it.

If anything, I need to know how to figure out which specific cdC and cdJ files to delete so new ones will be created. There are thousands of files in that folder, and it is not simple or conducive to delete them all every time the system fails to reflect my changes.