That sounds a bit rubbish to me.
I had jabs twice a week for about 6 weeks when first diagnosed. I had no B12 in my system at all though. You have stores normally for about 2-3 years in your liver. The stocks take a long time to deplete. I would think your baby is fine.
I did worry a lot though when I had my 1st baby, as my levels plummeted as soon as I got pregnant. I never had a clear answer out of anyone at either hospital I was attending to get advice about how to deal with it. My GP did wonder if it's because you have more blood in your system when you are pregnant. They did stabilise at about 6 months though. I was having monthly injections at the time and then every 2 weeks for the last few months. My 1st baby was fine.
The only thing I could suggest is that you ask for regular blood tests to put your mind at rest. I had monthly blood tests.
How did they test whether you have intrinsic factor, out of interest? I had the schilling test and didn't know there was another way of checking. I had to wait ages for my schilling test as there was a worldwide shortage of intrinsic factor at the time! No one ever mentioned an alternative.
I'm 9 weeks pregnant now. I had my annual B12 check just before I got pregnant. They were OK, just. I haven't seen a midwife yet, but I'll probably see one in the next few weeks and get another blood test.
I'd be interested to see how you get on. I'm moving house on Friday, so my computer will be packed up tomorrow and then out of action for a few days. Do post to let me know how you are gettting on.