Nighttime correction of $CO_2$ flux is one of the most important and challenging tasks in eddy covariance measurements over a complex mountainous terrain. In this study, we have scrutinized the quality and the credibility of the $CO_2$ flux datasets which were produced by employing three different methods of nighttime correction, i.e., (1) friction velocity ($u^*$) correction, (2) light response curve (LRC) correction, and (3) advection-based van Gorsel (VG) correction. The whole year datasets used in our analysis were collected at the two KoFlux tower sites (i.e., GDK deciduous forest site at the upper hill and GCK coniferous forest site at the lower hill) located in the valley of Gwangneung National Arboretum in central Korea. The resultant magnitudes and patterns of ecosystem respiration ($R_E$), gross primary productivity (GPP), and net ecosystem exchange (NEE) of $CO_2$ showed marked differences among the datasets produced with three different correction methods, which were also site-specific. The examination from micrometeorological and ecological perspectives suggests that the major cause of some inconsistency seems to be associated with the advection of $CO_2$ along the sloping terrain and the inappropriate selection of the correction data that might have been already affected by advective flows. The comparison with the results from other studies indicated that the overall characteristics of the corrected $CO_2$ fluxes at GDK and GCK (except those with LRC correction) were well within the ranges reported in the literature for various ecosystems in East Asia in similar latitudes. However, our study also implies that there will be always a room for further improvement in the present datasets. Therefore, caution must be exercised for the data users in order to properly use the updated version of datasets through transparent, open and participatory communication with data producers.