So I'm not really sure what you are trying to say but here's a breakdown in terms of the iteration:
Using uncorrected value:
Iterate all loops simultaneously with one set of values
Using corrected value:
Iterate first loop
Obtain corrected value for junction
iterate second loop using corrected value obtained from first loop without modifying any other flow rate
Obtain corrected values for all pipes
So no, you don't have to make changes to the other flow rate to balance them though you probably can and it would probably speed it up. I'll try it and get back to you