There is no book that lists losses for all transport units but some are mentioned in detail in “Battle of France, Then and Now” by Peter Cornwell.
As it happens, Larry deZeng and myself have been developing a book about Transport Unit Histories of the Luftwaffe, and as a byproduct we have scrounged up a lot of detail. At this point in time we are quite a ways from getting this published, but I can tell you that if you want loss statistics your best bet is to visit:
www.ww2.dk and look under Transport units. Go to the bottom of the page for each unit and look at:
“Flugzeugbestand und Bewegungsmeldungen”. This will bring up a table of month by month losses and inventory statistics per Gruppe. This is a very informative feature.
Apart from that, you might have to resort to looking through the microfilms of loss reports:
RL 2 III Gen.Qu. (6. Abt.) Meldungen über Flugzeugunfälle und Verluste.
I hope that this helps
DGS