Puest, Carsten (1999). Egyptian phonology: an introduction to the phonology of a dead language. Monographien zur ägyptischen Sprache; 2. Göttingen: Peust & Gutschmidt.
This monograph which describes the history of Egyptian phonology is invaluable to the field of Coptic phonology. It includes discussion of the phonological changes that occured in Coptic and the effects the Greek and Arabic languages have had on this. It has fortunately been digitised and made freely available by Heidelberg University here. I suggest you consult section 2.2 (pp 30-32) in the first instance as an introduction to Late Coptic phonology and Bohairic in particular, although the whole work is of importance.