No the individual lines cannot be resolved (Even if the spectrometer had enough resolution they would be broadened in the stellar spectrum to the point where they merged). The depth of the merged bands however gives a measure of the spectral class and therefore Teff even in low resolution spectra. The referenced Atel for example just used photometry in a particular targeted 705nm waveband to estimate the temperature change.
“Measures of Wing TiO-band (705 nm) and near-IR colors indicate that currently Betelgeuse has relatively strong TiO-bands and has a corresponding lower photospheric temperature of T~3580 K (relative to T~ 3660 K near maximum brightness”