We have an extension which was initially installed via Magento Connect. Since then the extension was modified locally, and there have been several patch releases from the vendor. Upgrading the extension via Magento Connect would no longer work, so I did the upgrades locally (unzipping the package and re-applying our changes, etc).
After upgrading the extension I've found that the update is live and running, and the core_resource table in the database has registered that it's upgraded. However, I noticed that Magento Connect still thinks I'm running the previous version.
Where does Magento Connect track which versions have been installed? Since I'm no longer using Magento Connect to upgrade this extension what steps should I take?