Travis,
You are so young. CD means Change Directory; it is a command-line (DOSBOX, Powershell) "tool". As for why you would want to downgrade a device driver, if the upgraded device driver has added a problem that is affecting how you work (or play), then you downgrade to a version that doesn't have the problem until it is properly fixed.
The Chipset Software (a.k.a. INF Update) package does not actually contain or install any device drivers. Instead, what it is doing is installing .INF files that tell Microsoft-supplied device drivers how to optimally support a particular (Intel) device. In this case, it may be that one of the .INF files says something that it shouldn't or no longer says something that is should. Regardless, whatever version of this package was installed originally, it failed to update (read: provide information about) these Root Ports. By reinstalling this package (and using the "-overall" flag to force over-install), the entries for these missing devices will be installed. Now, if you are bothered by doing a "downgrade", you can look for a newer version of this package on the Intel downloadcenter site of you wish. The link I provided points to the master release - which should be good enough, but their admittedly are update(s) available. The problem with installing these updates may be that your motherboard manufacturer may not have had a chance to validate these updates. You should really be installing whatever version your motherboard manufacturer provides on their web site.
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