Do I understand you to mean that your hen is continuing to sit to hatch rather than rising to raise the chicks?
By, what, day 6 now? Yes, she should be up and leading the chicks to water and teaching them to scratch and be chickens.
She might be doing that when you are not looking, but it would concern me as well that these chicks are not thriving like the ones in the incubator/brooder.
I suspicion disease...either coccidiosis or bacterial. The coop is hardly sterile, and neither is your indoor brooder, but it would may be more so. Something may have taken hold in the chicks with momma if these are full siblings to the ones in the brooder. (If you've got different breeds/strains there may be other factors).
I would put the broody chicks on something like Sulmet which addresses both the major bacterial infections typical at hatch (eColi, Salmonella) as well as Coccidiosis.
If momma is hesitant to get up because they are unthrifty, this may address that. Otherwise, momma is not shifting into raising mode, and you may need to intervene by taking the chicks to brood them yourself.
Occasionally a hen will fail to shift into raising mode and not take care of the chicks. However, if you placed started fertile eggs under her before she had fully set (ie started them in the incubator then gave them to the hen), if you interrupted the time schedule, then the hen will frequently want to continue to sit as her time clock tells her she should be setting and not raising. Not too many foster broody mommas will finish a started clutch and respond properly if the time clock has been shifted by more than a few days.
You are correct with what you were thinking. Initially I had a pullet sitting on this batch of eggs for about 12 days. Then 2 other girls decided to get into the nest with her. So at one point their were 3 girls sitting on these eggs together. The original sitter decided she had enough and quit being broody. Then 1 of the girls decided she wanted her own nest and she left to go sit in a different box. This left this one pullet on the nest for the last week of incubation and hatch. So her clock most definitely could have been off. She only sat on them for a little over 1 week. She was not switching to raising mode, just sitting on the chicks whenever I watched her. I put her back in the coop and run and she went right for food and water and mixed back into the flock. I've got 2 more girls sitting on 2 seperate nests, so I'm sure you guys will hear from me again!