I like the previous suggestions of Oriana and Mavis, but I think Mavis still lacks that spark and there’s something about Oriana I just don’t love. I think another PP made a good point of bridging the gap between James and Atlas!
Some that come to mind (I apologize in advance for any repeats):
Allegra - this is an Italian naming meaning joyous. I think it’s just beautiful and would compliment your boys’ names nicely. I don’t love repeating initials though.
Amity - I know I just said I don’t like repeating initials but this is such a bright pretty name that means friendship! I’ve met only one girl with this name, so it’s fairly unique, but very wearable at any age.
Avalon - I don’t love this one but I think it sounds cool with James and Atlas and it’s very unique in sound and popularity, yet has familiar elements of Ava and Evelyn.
Briar - I’ve always had a soft spot for this name. While I don’t think it’s the perfect match stylistically, I don’t think it clashes and I think it would add a unique, naturey element to your set.
Briony/Bryony - I love this one and I think it would pair really nicely with your boys! I’ve never met anyone with this name but I think it’s charming and girly without being too frilly. I slightly prefer Briar though with your set.
Calla - I much prefer this to Callie or other feminine names with this sound. I think it has the short punchiness that James and Atlas have while still being soft and feminine.
Cosette - I think this ties in well with the strong consonant and distinct “s” sound found in James and Atlas. I think, like Calla, it’s softer than some other options.
Ophelia - I adore this name! I think it has the old, classic feel of James and the charm and history of Atlas while still being distinctly feminine. It’s also different without being unrecognizable. A gem of a name!
My vote would be for Briar first, followed by Cosette, but I still think Amity and Ophelia are strong contenders. They all offer and bring something different to your sibset and each is unique and feminine. It just depends on what you’re looking for!
James, Atlas, and Briar
James, Atlas, and Cosette
James, Atlas, and Amity
James, Atlas, and Ophelia
I think whatever you end up deciding will be perfect for you and your family and make a really love match with your boys! Best of luck 