I want to reintroduce them, but I'm not sure how closely this reintroduction needs to follow the usual introduction protocol. I know I need to give them plenty of space, but do I need to wash their bedding and fleece hideys with vinegar if they've been in the same cage this whole time? If I do, do I need to wash all of their bedding and fleece hideys in vinegar, or just what I need for their reintroduction and the first week or so of living without the fence again? After they've been reintroduced, will putting up the fence while they eat their pellets and hay undo any of the progress made in their reintroduction? Penny is a very fast eater, so the fence is necessary in order to ensure that she doesn't take more than her share of the food.
In case it matters, Penny has always been the dominant pig because I brought Lily home when she was only five weeks old and Penny was three and a half. Their initial introduction was therefore very peaceful. Lily had started trying to assert dominance once every month or two, but since Penny is so much bigger than Lily, Lily always gave up after about half an hour to an hour.
While it looks like it won't be a seamless reintroduction, making it look like a whole new space might be good. Oh, and mix up the location of objects like waterers and bowls to new locations so it seems new.
The other thing that will help a lone piggie is putting them as close to the other cages as possible. Even though he or she doesn't like sharing their space with a cage mate, they still enjoy knowing that the other piggies are there. Guinea pigs in separate cages usually copy and learn behaviors from each other, as it is still a social environment for them. I have 6 cages with 12 piggies in them. 4 of them have a pair of 2, one has a trio and Mr Bubbles is the loner. What I have is basically 6 cages of guinea pigs all doing pretty much the same things.
I'm not telling you to give up, by any means. What I am saying is that you should have a plan in place just you can't get them paired back up. Good luck and I hope it works out for you!