Hi Ruben,
If you copy the mojoportal-core.sln to a new folder, rename it to mojoportal-ruben.sln and then put it back in the root folder and open it. Now you can remove the projects for the data layers you are not using. Then you should be able to continue using svn update with no problems and your solution will load and build a little faster. You don't want to actually delete the files, just remove the projects from your custom solution. If you delete the files then you do svn update they will most likely come back again.
Best,
Joe