Any programmed gas switches are taken into account when Cobalt calculates decompression and ascent time. However, if you dismiss a gas switch alert dialog without making the switch, Cobalt will recalculate your decompression schedule based on the current gas mix.
For deep and exceptional exposures (decompression dives below 150'), you will not see deep or safety stops. The algorithm will incorporate them into the required deco stops, which must be observed.