We had sort of a similar situation happen. We ordered 10 ducklings from an online hatchery. 1 of them died the first night

The hatchery was happy to replace the loss but can only ship in sets of 2 or more. So, they shipped us 2 ducklings. Well, one died in shipment. So, with shipping times and such I had a group of 9 ducks that were hatched on the 9th, and one single duckling that was hatched on the 17th. Anyone who's had ducks knows how much of a difference 1 week makes!! So, we tried to put the baby into the flock - which we were brooding in a 150 gal 2ft tall stock tank. Well, the olders just TRAMPLED her and picked on her! We immediately had to figure something out! So we put a Tupperware bin into the stock tank so she was "with" them but they couldn't get at her. After 2 weeks, incorporating her still wasn't working. They picked on her, trampled her. So, we put up a partition in the tank with hardware cloth so that they could touch and smell but still not hurt each other. Well, even that didn't seem to help when all in one area! But, at 4 weeks, my husband and I couldn't' stand the smell and noise any longer so we decided it was time for these ducks to move out!!! We have a very large covered shed that we converted into duck masion, ran heat lamps, etc.. we put her in with the big ones then all at the same time and have had zero issues! I think it was something about putting her into THEIR house, rather than it being all their big new house. I think "territory" has a lot to do with it!
Now, our 5 week old ducks aren't enough for us! we love love love! so we're looking at adding 2 cayuga into the mix - straight run (which is scary!). But, what I'm thinking is to keep them in the house for a few days till they are a bit stronger. Then, put a dog kennel (one of the big metal ones) in the duck mansion so from the start they are all kinda in everyone's house and can touch, smell, etc.. from the very beginning. Sometimes I wonder if the plastic tupperware divider hurt us because it just delayed the touch/smell sensation that I think is so important. What do you think?