Hepburn doesn't use the apostrophe for that. The apostrophe is for words with a glottal stop like ze'tai. Or without an apostrophe as zettai is possible too.
>ほんい hon’i
>ほんやく hon’yaku
http://park.itc.u-tokyo.ac.jp/eigo/UT-Komaba-Romanization-of...
Also, where the hell did you learn your Hepburn?
The Genki books seem to not use apostrophe but a dash, since I found a PDF of it and it uses the terms "on-yomi" and "kun-yomi" to distinguish んよ (n'yo / n-yo) and にょ (nyo). It also very clearly says that った becomes "tta" right in the beginning, so I have no idea where your apostrophe usage comes from.
港南 has a very unambiguous Hepburn romanisation of kōnan, which is impossible to confuse for こなん ("konan") or こんあん ("kon'an" / "kon-an").
A glottal stop is like "uh oh", where you stop the air with your glottis.