Linking assets using external SVN in unity

I did some modifications to my project (changed file name`s) and did a test run and it works fine. I then committed my modifications to the server re-downloaded my new project from the server and all the links between my objects are gone. I have read some stuff about using unity with external version control (http://unity3d.com/support/documentation/Manual/ExternalVersionControlSystemSupport.html) and working with assets in unity (http://unity3d.com/support/documentation/Manual/Working%20with%20Assets.html).

The documentation provided seem to conflict a little bit since the first documentation implies that only the .asset files should be checked into version control and the other states that the metadata files are important for establishing the links between all your assets.

I did a little debugging of mine and found out that if I replace the metadata folder and guidmapper file of the project downloaded from the svn with the metadata folder and guidmapper file of project I did a test run with it seems to fix the problem.

Is it advisable for me to go and check this into the version control