Hello meshmixup,
Align chunk procedure only orients chunks relatively to each other based on the selected option (point based, camera based or marker based) and doesn't change camera positions anyhow. However, badly positioned cameras could induce errors to chunk alignment, so it's recommended to disable them prior to Align Chunks procedure to get correct result.
But to fix wrong camera positions I can recommend two options:
1) reset camera alignment for such cameras and then use Align selected cameras option.
2) Export cameras from Tools menu from correctly aligned chunk and use Import cameras option for other chunks, but in this case not only naming convention should remain the same, but also all camera positions and parameters should be unchanged compared to the "reference" chunk.