Windows keeps your cookies in two places:
Rather than searching for the folders yourself, you can also go Tools and Help tab in Dutch Duck IE History Viewer. There is a button "Special folders", which will show the path of the cookies and the temporary internet files folder.
The files in the temporary internet files are pointers to the actual cookies that are located in the Cookies folder.
If you delete a cookie from the Cookies folder, either through the Dos-prompt or through Windows Explorer, it will still be in your Temporary Internet Files folder and Internet Explorer can still use the cookie
If you delete through Windows Explorer a cookie file from the Temporary Internet Files folder, both the pointer to the Cookies folder and the cookie file located in the Cookies folder are deleted. This is exactly what Cookies Explorer does, when it deletes a cookie.
If you would manually remove from the dos-prompt the entire Temporary Internet Files folder (the way to do this would be very similar to the way you can remove a corrupted History file), the next time Windows reboots, it will rebuild the cookies in the temporary internet files folder, using the cookies that are in your cookie folder.
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