I looked this up using the archive with a search for ties alternative ending
here is the link to the workaround. I noted also that lyrics have the same problem while working a guitar score with alternate endings. The author indicates it is for version 2.1.6 but I am using 2.3.8 and have the same problems.
http://lists.gnu.org/archive/html/bug-lilypond/2004-01/msg00037.html
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