Flash Player is not an extension therefore, will not show up in the extensions list. It does show up in the plugins list (opera://plugins)
Also, I don't see Opera version 41.0.2353.59 on the Opera site. I see versions 41.0.2353.56 and 41.0.2353.69, but no version 41.0.2353.59. The latest Opera stable version is 42.0.2393.351, released yesterday. Unless there are compelling reasons to remain in previous versions, it's always best to update to the latest version.
I am using the developer version 44.0.2475.0 because there is currently a trojan in the desktop stable version, I tried four times today to download it and Webroot caught the .exe with a trojan every time. Also because it has been absolutely terrible with invalid certificate validation and non-loading images. Maybe because it it an illegitimate version (41.0.2353.59).
Can you give me the full path of the plugin folder? There is no plugin folder in either the Opera program folder or in the Opera Developer folder.
According to the link of all Opera versions there is no version 184.108.40.2063.59 listed there. From where did you download 220.127.116.113.59? I would recommend you contact Opera support regarding the alleged trojan in their installer. It's also possible Webroot is reporting a false positive, but then again, if you have a version that doesn't exist it's possible you have a malicious installer.
If you go to opera://plugins and click the Show Details button in the upper right it'll display plugin details, including the folder path. For Flash Player the path is C:\WINDOWS\SysWOW64\Macromed\Flash\ (64-bit OS), or C:\WINDOWS\System32\Macromed\Flash\ (32-bit OS). If the file name is pepflashplayer32_24_0_0_194.dll then you have the latest Flash Player version installed.