Making sure I got this correct:
1) You have a CSS (as a Resource with no Template) and want to import chunks so that you can make quick edits to change the entire look of several styles (like theming). However, since you upgraded, the resource no longer parses the chunks.
2) As a workaround, you created a file version which loads, but is completely static so the chunks cannot be read.
Assuming that I got this correct, the issue is really simple to solve. You have multiple ways to accomplish this. If you want the CSS to be parsed, it must be a Resource (unless you want to manually force the parser).
Move it back into the Resource. Second, set the Content Type (on the Settings Tab) to "css". Once it is set to CSS, you have a couple of options. The old tutorials for CSS as a Resource tell you not to use a Template. This information is outdated and no longer required. Not using a Template actually limits you in Revo 2+.
You can set it to use a Template and it will be parsed in full by ModX. Simply make a Template that only has
and set your CSS Resources to use the new Template. This should resolve any parsing issues you might have. (I actually have my CSS Template run a couple of Snippets and process Template Variables!) It will still "render" fully as CSS for you as long as you have the Content Type set to "css".