So if you get "File GUID does not match" it means you have done something to break your project metadata.
Common ways this happens is -
1. Moving files outside Unity. This is one of the key things in Unity - never move files in a project from outside Unity. (
http://wiki.unity3d.com/index.php/Moving_and_Copying_Unity_Assets)
2. Sharing Unity projects between computers via dropbox / etc. without meta files turned on.
3. Using version control without meta files turned on.
Once metadata is broken, as far as I'm aware, it can't be fixed.
You can still update tk2d, but you'll have to do it manually. I"m assuming you haven't run the "Setup for JS" script and that you're using c#.
1. In your exiting project, enable meta files, close down Unity, and make a zip backup of Assets & ProjectSettings. Libraries isn't needed with meta files on. You'll notice a LOT of .meta files in there.
2. Import tk2d 2.0 into the project, letting it overwrite what it needs to. Restart Unity, and fix any errors as described in the migration guide.
http://unikronsoftware.com/2dtoolkit/doc/2.00/migration_guide.html3. Hopefully your project would have updated fine.
If you wish to do this, but you've run Setup For JS - you should do this instead.
1. Create a new project, do NOT turn on meta files in this project.
2. Import 2D Toolkit 2.0 into this new project, and then after its imported properly, run Set up for JS.
3. Shut down Unity, and browse to that folder.
4. Copy the contents of the Tk2DRoot folder and its subfolders, taking care not to overwrite the meta files in your original project.
5. Copy the contetnst of the Plugisn folder and its subfolders, again taking care not to overwrite meta files in the original project.
6. Fix any compatibility issues as in the migration guide.
Let me know if you run into any more issues - unfortunately your project is now "broken" compared to the default 2D Toolkit project, and its going to be tricky updating.
Note:
If you have messages showing "associated scripts can't be found", then you will need to drag the appropriate scripts in to fix it. If you're going to do this, you might as well delete all the tk2d files, reimport the package and fix them then once and for all. That WILL actually fix the meta files and you'll then be able to upgrade the normal way.