Here I will walk you through the process:

• Alright so I have a bunch of forms like this: http://i.imgur.com/1O3Uc.png
  
• I select them all and check out and I get this error: http://i.imgur.com/CbZ4q.png (this is normal. this happens to every changes I merge and there are no problems in-game)
  
• I then select them all again and check in and select my master file to merge the changes to. Normal version control stuff.
  
• Normally the list I linked in step 1 empties out because all those forms are now in the master file. This time it still looks exactly the same. And the changes do not appear in-game.

Another case of this is when I was landscaping. I created some new landscape and put some rocks and trees and etc. When I tried to merge the changes I would get a bunch of errors like in step 2. I usually only get 1-3 and no more but with this plugin file I get around 10. And then when I look at my landscape with the master file active and not my plugin file(which contains the rest of the landscape changes I made) it would look like this: http://i.imgur.com/0rjbF.jpg
As you can see the terrain has stopped at a certain point and now there are floating objects and stuff.


So how can I fix this?
Is there a way to "force" VC to merge these changes?
Are these forms somehow corrupted?
Did I do something wrong? If so can it be prevented in the future?

You can prevent that error by re-generating the FID and FUD files of the ESM you merge to. Perhaps a retry of the merge automatically does that, I never tried that. I think re-generating manually is safer though.

However, the real culprit here is that you are trying to merge changes to forms that originate from Skyrim.esm. By default the Creation Kit does not allow this, even though you try to merge the changes into your own ESM. I explained how to circumvent this restriction in the tutorial I posted on the CK wiki:

http://www.creationkit.com/Version_control#Trick_to_check_out_Skyrim.esm_forms

oh! of course.

Thanks, I will test this when I am not busy and report back ASAP.

It seemed to work! Awesome!

Is it safe just to keep the 8th byte at 01 instead of 81? Or should I switch back when I'm done merging and then switch back every time I merge?

Probably wouldn't hurt when modding, but ingame it's probably messed up majorly. I haven't tried either though.

You could just have a second copy with the byte at 01, then you can just switch it with the vanilla file whenever you need to merge?

Yep just thought of that too. I'll just keep a 01 version in the merging folder and when I play I replace it with a 81 version that I have backed up.

Thanks so much! And good luck with merp