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AccessAide use is probably unrelated. I will investigate why the guide section of the opf was not updated by the splitting.
One question, is this by chance an epub3? If so did you use the epub3 tool to generate a NCX and update the guide? If not, please do that. Any existing guide section, and NCX are NOT updated by splitting as under epub3 these are replaced by the NAV and not used.
To force them to sync with the NAV you must use that tool to rebuild the guide and NCX.
On epub2, this would be a bug as both the guide and ncx should be updated.
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