I deploy Adobe product updates with SCCM 2012 R2. When the Flash Player 16 updates deployed to my Windows 7 desktops, the Plug-in and ActiveX versions of the product were un-installed and only the Plug-in version of Flash Player 16 was re-installed. Here is a copy of the relevant section of FlashInstall.log file:
=O====== M/15.0.0.223 2014-12-29+16-09-47.840 ========
0000 00000010 "C:\WINDOWS\TEMP\{5B22FAE3-C7CE-46D3-8AC1-D9707D61DD8D}\InstallFlashPlayer.exe" -uninstall plugin
0001 00001037 SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\Adobe Flash Player Plugin/ 2
0002 00001037 Software\Microsoft\Windows\CurrentVersion\RunOnce/FlashPlayerUpdate 2
0003 00001037 Software\Macromedia\FlashPlayerPlugin/ 2
0004 00001037 Software\Macromedia\FlashPlayer/FlashPlayerVersion 2
0005 00001037 Software\Macromedia\FlashPlayer/SwfInstall 2
0006 00001021
0007 00001036 Software\Macromedia\FlashPlayerActiveX/PlayerPath 2
0008 00001036 Software\Macromedia\FlashPlayerPlugin/PlayerPath 2
0009 00001036 Software\Macromedia\FlashPlayerPepper/PlayerPath 2
0010 00001036 Software\Macromedia\FlashPlayerActiveX/PlayerPath 2
0011 00001036 Software\Macromedia\FlashPlayerPlugin/PlayerPath 2
0012 00001036 Software\Macromedia\FlashPlayerPepper/PlayerPath 2
0013 00001037 SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image File Execution Options\\FlashPlayerApp.exe/ 2
0014 00001037 Software\Microsoft\Windows\CurrentVersion\Control Panel\Extended Properties\System.ControlPanel.Category/C:\WINDOWS\system32\FlashPlayerCPLApp.cpl 2
0015 00001036 Software\Macromedia\FlashPlayerActiveX/PlayerPath 2
0016 00001036 Software\Macromedia\FlashPlayerPlugin/PlayerPath 2
0017 00001036 Software\Macromedia\FlashPlayerPepper/PlayerPath 2
0018 00001036 Software\Opera Software/Last CommandLine 2
0019 00001036 Software\Opera Software/Last CommandLine 2
0020 00001036 Software\Opera Software/Plugin Path 2
0021 00001036 Software\Opera Software/Plugin Path 2
=X====== M/15.0.0.223 2014-12-29+16-09-48.450 ========
=O====== M/16.0.0.235 2014-12-29+16-09-53.488 ========
0000 00000010 "C:\WINDOWS\TEMP\{46C4790E-CA51-4D6C-AEF0-327A3674AADE}\InstallFlashPlayer.exe" -install -skipARPEntry -iv 2 -au 4294967295
0001 00001036 Software\Macromedia\FlashPlayerPlugin/Version 2
0002 00001036 Software\Macromedia\FlashPlayerPlugin/PlayerPath 2
0003 00000020 C:\WINDOWS\SysWOW64\FlashPlayerCPLApp.cpl
0004 00001037 SOFTWARE\MozillaPlugins\@adobe.com/FlashPlayer/ 2
0005 00001037 SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\Adobe Flash Player NPAPI/ 2
0006 00001037 SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\Adobe Flash Player Plugin/ 2
0007 00001036 Software\Opera Software/Last CommandLine 2
0008 00001036 Software\Opera Software/Last CommandLine 2
0009 00001036 Software\Opera Software/Plugin Path 2
0010 00001036 Software\Opera Software/Plugin Path 2
0011 00000014
0012 00000015 C:\WINDOWS\system32\Macromed\Flash\FlashUtil64_16_0_0_235_Plugin.exe
0013 00000024 C:\WINDOWS\system32\Macromed\Flash\plugin.vch
0014 00000019 C:\WINDOWS\SysWOW64\FlashPlayerCPLApp.cpl
0015 00000012
=X====== M/16.0.0.235 2014-12-29+16-09-54.254 ========
Thanks,
Matt