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This should not happen, unless you have set Preferences -> Conversion / Common Options -> TOC -> Force auto-generated TOC. If this is set, try unsetting it.
If an ePub has a TOC, there is usually no need to auto detect chapters (they are already in the TOC). Unfortunately, quite a few ePubs don't have a TOC (in a crime against ePubs) - so auto-detecting is necessary. You would not normally force the use of the auto-generated TOC unless the ePub's original TOC was not good enough.
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