That's one of the reasons this site is against petstores. Chances are they had males in with females and all females of age are pregnant. That means the other one is too
if it's actually female. 2nd problem with petstores they are absolutely horrible at telling the gender of animals like guinea pigs. You need to double check that your other pig is actually female before putting them back together. There's a sexing page with pics on
Index of / and here:
Guinea Lynx :: Sexing Pups. If it's a male then the one that just gave birth could already be pregnant again. The female immediately goes into heat after recovering from labor(sometimes just barely recovering) and the male will get her pregnant that same night. If it's female then it's probably pregnant as well. You can leave females together even with newborn pups. They do not have to be seperated unless 1 female shows signs of being overprotective and wants more space. The only risk to leaving 2 pregnant females together is that the one not giving birth may help the other one to clean the pups and eat the placenta which contains hormones that can cause the 2nd female to go into labor prematurely. At this point there's no reason to seperate them so long as they get along with each other(provided they are both female).
Next step after you determine what gender of pigs you have is to read over the care guide.
Guinea Lynx :: Guinea Pig Care Guide