Just for the record, guide elements are never useless under epub2. IMHO, A well designed epub2 should use the Sematic setting features of Sigil to set major structural parts of the epub that will appear in the guide. This is especially important for reading software for the visually impaired.
The "best" solution for epub2 is not to remove the empty guide but to use it to properly set the major structural parts of the epub2.
Under epub3, this information has been moved to the machine parseable nav so under epub3, a guide can be empty and if so is already removed by Sigil.
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