As Mark guessed, I am indeed setting up the junction points by hand. This is how I made it:
-Create folder D:\SVN -Do checkout on D:\SVN with "Immediate children, including folders", so only the folders come in and not their contents -Do "fully recursive" update on D:\SVN\SmallFolder to get its contents -Create folder E:\SVN -Do checkout on E:\SVN with "Immediate children, including folders" -Do "fully recursive" update on E:\SVN\BigFolder -Remove the .svn folder from D:\SVN\BigFolder to make it actually empty (required for junction points) -Create junction point from D:\SVN\BigFolder to E:\SVN\BigFolder That's it! To Windows Explorer, D:\SVN now looks like a complete checkout. However, SVN now gives the errors I posted previously. With kind regards, Joost