No, you are right, it is a bit complex to renumber the entire set of controls.
Personally, I would advise against renumbering controls. I think it's safer to leave controls with their original numbers all the way through the process, just to avoid any mistakes that would arise from having for example printouts before and after any renumbering of controls. The same goes for the control site markings in the woods. If these markings have an id number on them, it would be error prone to change it.
Well, this is my personal position, but I know it is advice that is commonly agreed.
To ensure consistency, Condes does not allow duplicate control numbers. Do you think this restriction should be lifted?
However, Condes DOES allow you to rename a control, and my immediate suggestion to achieve an even distribution of control numbers over the area would be the same as yours -- namely to start by numbering the controls temporarily in a different range, and then order them back into the final range at a late stage. That would to some extent also alleviate the above concern, because no new control would inherit another control's number.
Alternatively, if you have the controls in the final range, but need to rearrange, you could rename one control to a number out of range, then rename the control that is to take its number, etc.
Sorry, no silver bullet...
regards,
Finn