first of all, you shouldnt really have 2 females in one isolation. if one female drops the other female might eat them. mind you...the mother herself would eat the babies as well.
it is possible you have only 2 babies. but i would suspect the other female might ate it and left you with 2 babies. Females guppies also drop a few of babies at times...you have to play by the ear.
you can leave a female in insolation as long as you want. not as recommended as it will stress her out...but as long they are comfortable in there and not too tight, and getting enough circulation water movement in there.