Since this forum post comes up high in Google searches I should probably update that I found a way to make 3D videos into 2D. It will work every time however you have to set some things every-time. I have posted a bug in the Handbrake forums describing the problem.
https://forum.handbrake.fr/viewtopic.php?f=11&t=28127&p=129880#p129880
1) Download and install handbrake.
HandBrake: Downloads
2) Load the video=> Click on Source, open file, then navigate to the video file you want to "FIX"
It should be a 1280x270 video file where the two "eyes" are anamorphic-ally squished to half width.
3) Start with the "Android Tablet" profile
4) Under the Picture tab change the settings to
a) Anamorphic to "Custom"
b) Above make sure that Width=1280 Height=720
c) Below check that "Display Width" is 1280" (I'm not sure what the PAR stuff is)
5) Under the Picture Tab still change Cropping to "Custom"
6) Change Left to 640 (cuts off left "eye" leaving the right "eye" which is more centered in the camera/phone)
7)Check the "Size:" Settings again sometimes touching one will effect the other
8) set the destination file where you want the video to be outputted.
9) Click Start.
In theory I should be able to make this a Pre-set and be able to export that and upload the file and recall all of these settings. However the "picture" settings don't seem to save or stick. If you make all the settings then load a different video you will sometimes have to fix the settings. It's odd and Like I said above I have filed a bug about it. Here is the preset
https://www.dropbox.com/s/51s2bq31zikg6ma/3Dto2D.plist
Batch Processing: You can batch process more than one file.
1) click source
2) Open Folder
3) Select the Folder
4) under title select the video file you want to convert.
5) fix the picture settings listed above
6) Click "Add to Queue (changing settings after the file has been added to the queue wont effect video files already in the Queue)
7) Select the next video "source" under "title" and repeat.
8) If you would rather you can select each video change the picture settings then click on the arrow pointing down next to "Add to Queue" you can select to "add all" files from the folder.
9) of course click "start" to start "Fixing" the videos.
I'm not a handbrake expert I just had to figure this out on my own and that was painful so I'll try and save someone else the pain.