The .NET patches are particularly messy, so much so that Microsoft's advises:
To work around this problem, temporarily remove the September 12, 2017, Security and Quality Rollup update, and then install the corresponding September 12, 2017, Security-Only update to make sure that systems are secured against the latest vulnerabilities.
I was four for four: 1.) I re-enabled libraries prior to installing the KB4038777 patch, and this was sufficient to prevent the folder rename bug that occurred after this rollup was installed on my work machine. After testing, I disabled libraries again. 2.) I checked and my C:\Windows\System32\oem folder was not touched. 3.) I launched IE. Immediately a message appeared at the bottom about tabs being placed on a new row. I clicked the Revert button faster than you can say "Ask Woody". IE then appeared normal. 4.) I launched Paint.NET and encountered no issues.