My Aloe vera flower is in full bloom, and some of its petals are starting to fall. It also has some sprouts.
Should I wait until the flower has completely died down to re-pot the new sprout?
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You can do it right now if you like. No need to wait at all.
Those "pups" - the new plant sprouts you're talking about - can likely be removed without needing to disturb the main plant itself much. Often you can just dig carefully around it and separate the pup from the main plant, then pot that pup in its own container.
If you wish to re-pot the main plant itself, you can certainly re-pot it while it is in full bloom. They are pretty sturdy plants.