Loosing external reference when Grouping/moving Code

One of the most difficult or time consuming task is to keep our code organized has it evolves. I do not know about others but our code is evolving with time as we encounter new options and configuration for our hardware. Sometimes a modification starts with the addition of a few functions but after few month we end up with a real spaghetti very difficult to troubleshoot. Since often those modifications are done under the gun during commissioning it is not easy to know where it is going to go.
The biggest reason why it is difficult to re-organize a code after the fact are all the external references of the objects. If we decide to move them into a new or existing function group to help clean-up the code all those connections are lost and we need hours to re-create them. That is if we where smart enough to first identify them. More specifically I am referring to:
-Display object
-Adjust group
-Log object
-measuring object
It would be so much nicer if those connections could be kept.