Wanted to post this here in case others may have a similar issue. We recently found that after running the commands to remove files AND the Macromed\Flash folder, some of our Windows 2012 and Windows 2012R2 servers would stop having patches applied.
The BigFix action to install the patch comes back as Complete. After a reboot of the server and for a period of time (seems like an evaluation cycle) the patches are Not Relevant. Then they become relevant again. This is very difficult to determine with Action Status as well as Action History unless you then compare that with Relevant patches after a period of time following a reboot.
Per the link, I have created content to create/recreate the Macromed\Flash in System32;SysWOW64 folders. Attempted patching with reboots and this seems to have corrected the issue.