I can't help with your problem directly, other than to say you are not alone. You get the same loss of URL links when you do a ctrl+e, ctrl+s, ctrl+e.
See link to reproduce in std 6.0.1 mail file. ->
http://www-10.lotus.com/ldd/nd6forum.nsf/DateAllThreadedweb/c13e020d0357f8b585256def0052e236?OpenDocument