The solution is, luckily, not too difficult:
- save the edits to a patch
svn diff > great_mother_of_all_patches.patch
- revert the project to the last commit:
svn revert -R .
- apply the patch edit by edit (I know this is tedious) using the eclipse "Team Synchronizing" perspective, then click on the Synchronize button and choose the Synchronize with patch option
Disclaimer: I don't use the Eclipse subversion plugin because, on Linux at least, it frequently crashes Eclipse.