Amber only have the upper part of her body and Liz losed at least one leg in the water, so unlikely but you had me woried for a second ... ^^
I'm pretty sure that during the transformation from human to superhuman the body is fully restored, including limbs.
I think the only important thing is that there is a large enough piece of meat and head left from your body.
For example, Michael was in a pretty disastrous state before his transformation.
But after the transformation?
That's something else, especially if you're not the type gifted with regeneration.
For now, two possible explanations are offered.
1) The doctor simply swapped the lower half of the twins' bodies.
Which could turn out to be funny because both twins' pussyes liked a different type of sex
2) One of the twins was cut up for spare parts and the rest were thrown away.
A less likely option, since the remaining twin and Deryl would then definitely not want to cooperate with S.I.N.
But it is definitely one of the possible outcomes.