The precise control of alkali-metal concentrations in Cu(In,Ga)Se2 (CIGS) solar cells via post deposition treatment (PDT) has recently attracted attention. When PDT is performed at an elevated temperature, an accompanying annealing effect is expected. Here, we investigate how thermal annealing affects the redistribution of alkali metals in CIGS solar cells on glass substrates and the properties of the solar cells. In addition, we investigate the origin of non-homogeneous alkali-metal depth profiles that are typical of CIGS grown using a three-stage process. In particular, we use secondary-ion mass spectrometry measurements of the ion concentration as a function of distance from the CIGS surface to investigate the impact of thermal annealing on the distribution of alkali metals (Na, Ka, and Rb) and constituent elements (Ga and In) in the CIGS absorbers. We find that the depth profiles of the alkali metals strongly reflect the density of sites that tend to accommodate alkali metals, i.e., vacancies. Annealing at elevated temperature caused a redistribution of the alkali metals. The thermal-diffusion kinetics of alkali metals depends strongly on the species involved. We introduced low flux potassium fluoride (KF) to study a side effect of KF-PDT, i.e., Na removal from CIGS, separately from its predominant effects such as surface modification. When sufficient amounts of Na are supplied from the soda lime glass via annealing at an elevated temperature, the negative effect was not apparent. Conversely, when the Na supply was not sufficient, it caused a deterioration of the photovoltaic properties.