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I've just had the very issue.
In order to intermideately workaround this problem, I downgraded the svn-plugin back to version 1.5.4 as enabled by the plugins-management page.
Later I re-installed the new version of the svn-plugin in order to provide the log with the failure. Surpringly this issue did not occur again (neither the bug itself nor any relevant log-entry).
From what I remember and attribute to this bug:
1) Having a non-up-to-date version of Jenkins (can't remember which, though)
2) update all plugins
3) stop jenkins
4) perform the update of Jenkins (via aptitude install jenkins) to 1.550 and restart the jenkins-service
5) having the problems with the SVN configuration
6) downgrading svn-plugin back to 1.5.4
7) restart the jenkins-service (svn-settings of the projects where back again)
8) again update the svn-plugin to 2.1 and restart the jenkins-service
9) works
I have added the stacktrace from what I found in the log.
HTH