= Solution
The two measurements sample different atmospheric regions and different <radiative transfer> geometries. An <exoplanet emission spectrum> probes the dayside; an <exoplanet transmission spectrum> probes the morning and evening limbs of the <day-night terminator>. Several alternatives to an <exoplanet cloud deck> can therefore suppress the transmission feature.
* A cooler terminator has a smaller <atmospheric scale height> $H=k_BT/(\mu m_Hg)$, so the same change in slant <optical depth> produces a smaller transit-area change. A larger <mean molecular weight> has the same geometric effect. The assumption that the nightside <temperature> sets both limbs may itself be wrong.
* Genuine chemical heterogeneity can reduce terminator <carbon monoxide>. At lower <temperature>, <thermochemical equilibrium> can favour <methane> through $\mathrm{CO}+3\mathrm{H}_2\rightleftharpoons\mathrm{CH}_4+\mathrm{H}_2\mathrm O$, if local reaction times are sufficiently short. <Atmospheric photochemistry>, elemental abundance differences, and <horizontal chemical quenching> can modify this simple picture.
* The feature depends on a band-to-continuum <opacity> ratio, not abundance alone. A continuum enhanced by other gas absorption or a partly covered heterogeneous limb can mute the feature; the <two-limb transmission spectrum> illustrates this averaging. Stellar surface heterogeneity and measurement systematics can also bias an inferred feature amplitude.
* A strong CO emission feature can be amplified by an <atmospheric thermal inversion>, because the line forms in hotter gas than the continuum. It is consequently not an unambiguous abundance measurement without a simultaneous <atmospheric pressure-temperature profile> fit.
\b[Temperature, mean molecular weight, limb chemistry, continuum opacity and the dayside temperature gradient are alternatives or degeneracies to test.] In particular, the three-scale-height amplitude alone cannot establish different CO abundances between the hemispheres.
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