Did you reinstall your Adobe apps after updating the OS? You might try uninstalling CS4 (including Preferences), using the Cleaner tool (Google it) and reinstalling the CS4 suite. Be advised that CS4 is not supported in Yosemite and you may have other problems.
You really need to upgrade your InDesign version if you're a professional designer.
One file or multiple files? If the former, try exporting half of pages, then the other half to narrow done the culprit. And, probably a graphic with a bad font, or corrupt image.