Jose,
I would recommend testing your projects out in a complete new workspace on a clean install first. Here is a quote from one of the main support guys:
@support-scott wrote:
The best way is to download and install Eclipse 3.1 final and then MyEclipse 4.0M2 so that it points to it. Launch the new configuration on a *new* workspace. Then, you can test in parallel with your production configuration. If you want to see how your current projects work, just copy the directory containing them from your current workspace to the new one and then use File > Import… > Existing project into workspace to bring in the duplicate. Two completely separate environments will allow you to check stuff out without risk.
Then, if everything goes ok, you can point your new eclipse 3.1 install workspace out to your old workspace folder. And then those projects will be upgraded to MyEclipse 4.0M2. I would just always keep a backup copy of your old workspace in case something goes wrong.