I happened upon the above question incidentally and thought perhaps it is a good one to address since I study reproductive bats and many people who do not study bats might have the same question!
(to the right is a photo of a Jamaican fruit-bat late in her pregnancy)
The simple answer is yes, bats fly while pregnant. That said it is very energetically costly for them and they become increasingly awkward as the pregnancy progresses. Indeed they may be more likely to be eaten by predators as they become slower and less-maneuverable.
Not only do they fly while pregnant, but bats give birth to pups that are much larger relative to the mom's size than human mothers give birth to! So, they are still flying when the developing baby is larger relative to the mother than a human would be walking around with.
After bats give birth (upside-down which is yet another difficulty) the mother will occasionally fly with her ever-growing baby (most bats only have one pup per pregnancy although some have twins and more rarely- triplets). The fortunate bats like Mexican free-tailed bats (Tadarida brasiliensis) or other cave dwelling bats usually leave their young in the roost while they forage but some less-fortunate bats may have to move their young nightly or semi-regularly if they inhabit less-permanent roosts.
So next time you hear a pregnant friend or family member saying how their back hurts or it is hard to get around you can tell them to cheer up and remind them they are lucky that they are not a pregnant bat!
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