Hi Paul,
Till we finish the feature "Remove clouds"
there are no much options. If PHD2 loose the star during the dithering APT will consider that dithering is finished and will continue with the next step of what it is doing.
If the exposure has its own pause 10-15s and the star disappears on the 5th second of the dithering, APT will wait up to the end of the pause, so if the cloud is not huge, but just causing slight brightness change, PHD2 will be guiding when the next exposure is started
