I was in a very similar situation to you. I was having B12 injections regularly before I fell pg with ds1, a blood test showed my level to be 67, even though I was taking the pregnancy multivitamin containing it, my body still doesn't absorb it unless I have the injections, this in a condition called pernicious anaemia.

When I fell pregnant with ds1 my gp said to not have the injections whilst I was pregnant so I didn't, once ds1 arrived and the paediatrician did his checkup in the hospital one the of the things he asked me was if I had anaemia and when I mentioned pernicious anaemia he had my levels checked and they turned out to be about 160, so low, he said that it was very important to keep my B12 levels up with the injections as I was obviously not absorbing it orally (was taking multivitamins, and I'm not vegetarian) and that it was perfectly fine for future pregnancies to continue with the injections and that it would be worse for them to be too low.

So when I was pregnant with ds2 I continued to have the B12 injections every 3 months (so had 3 over the pregnancy), I checked with my obs as well and he said that it was fine to have them. DS2 is a happy and healthy 6 and a half month old baby now and I feel much better when I keep the injections up, if I don't have them I tend to get tired and feel run down.

Good luck I hope everything works out for you.