It turns out the User Libraries are maintained in a text file, not a binary file. If you get into this situation where the User Library dialog is unable to display its content, shut down Eclipse, and then start in the workspace directory and navigate to edit the file:
.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.core.prefs
and remove the offending "org.eclipse.jdt.core.userLibrary.MyLibTest=.. ." entry (or whatever your User Library name is).
Because the file begins with a period, Linux or MAC users will need to ensure they can find hidden files.
Thanks to the Eclipse team for providing the work around. The issue should be repaired in an upcoming version of Eclipse.
https://bugs.eclipse.org/bugs/show_bug.cgi?id=346002