i had the same thing happen with miss buffey after i had almost 2 weeks off from work over the holiday...she developed a case of separation anxiety too
... it had never happened before and it really worried me because she was not acting like herself at all ... i contacted her breeder and she explained it was separation anxiety
what she told me to do - and it helped within a couple of days - is to leave the room for a couple seconds, come back but do not make eye contact or do not acknowledge they are there (if you have more than one furkid, you have to do this to all of them, not just the one with the separation anxiety)...work up to a couple of minutes...make sure when you leave or enter the room, do not make a fuss, do not say goodbye or hello and avoid making any eye contact...then after the puppy settles down (stops barking, whining, etc), in a very CALM manner go to them and love on them
this will teach them that you will always be back for them...and by making them calm down before going to them, it should teach them that they need to be calm before getting attention...in miss buffeys case, i realized *i* was the problem - i made such a fuss coming and going (because i always had to say goodbye and give treats before i left and was always so excited to see them again when i came home from work) and once i stopped, the separation anxiety went away
anyway sorry this is so long and i hope this helps!
good luck with your baby....it will be tough because it makes you feel kind of mean ignoring them, but it is the best thing for them