Note that the NAV document in an Epub 3 has certain specifications it needs to follow. Stripping out the ordered list tags may not be the best answer in this case.
Sigil hides the numbering in its automatically generated nav.xhtml using css. namely:
Code:
ol {
list-style-type: none;
}
From your original comments, it sounds to me as if you may have inadvertently deleted either the link to the NAV's css, or deleted some inline styling that Scrivener output.