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I had a "regular" breakpoint at a line of code. I accepted changes from SCM. Breakpoint line # is now a method declaration. When running in debug mode, debugger stopped on method entry. However, I could not double-click in the margin to disable the breakpoint. The workaround was to find it in the breakpoints view and delete it there. I think I've also seen breakpoints end up inside comments and couldn't be removed in the editor.
*** This bug has been marked as a duplicate of bug 310478 ***