Hi,
I got it working, what I did for anyone who has a similar problem.
1. Import your new package into a new Unity project.
2. Don't play or run it.
3. Save project, not the scene, close Unity.
4. Check for .meta files in finder or windows folder, not the unity project ( shouldn't be any but if there are delete them).
5. Copy the files from the new project folders into the corresponding folder in old tk2droot. Don't copy the folder, copy the files.
6. Copy the new folders in the most recent package to the old package e.g : tk2dTileMap / tk2dUI and so on if you don't have them already in your current tk2droot.
7. Everything should work OK.
I had a conflict with tk2dTileMap so I just deleted the folder and it works OK.
Thanks.