It is not worth separating when you have a pair where transmission must have already happened. URI can usually be fended off by healthy piggies; it is typical generally for those with their immune system not yet fully developed or for some reason impaired (other illness, old age or pregnancy or major stress like bereavement/moves to a new home etc).
Just the added stress from a separation can make things worse - especially youngsters REALLY don't deal well with being on their own. These days the trend is to leave group animals like piggies and bunnies together as much as possible - including as company on vet trips.
Tips For Vet Visits
Young shop piggies are particularly prone to picking up URI and skin problems - they have been ripped from their families, have been kept squashed up with each other in close proximity during transport and at the back of the shop (makes transmission a lot easier) and are then sold on into a totally alien home environment as often very lost singles or baby couples with no older piggy to guide them...