Here is how I suggest you do this: when any segment entering a JB is 'touched' in a way that would currently cause a 'flag' to warn the user that the segment is locked, WME would instead 'take a quick snapshot' of everything involved in the JB and save that information.
A pseudo picture of the JB would be created where every segment entering the JB would be 'cut' where it crosses the boarder line of the JB.
The portion of each segment within the JB would retain the current segment # and other information as appropriate. The portion of the crossing segments remaining outside would be assigned NEW 'temporary' segment # and get their data as if the segments had actually been cut at the border at the time the JB was originally created.
When a 'save' is done, the process would be reversed with restoration of original data where nothing has been touched. Where changes were actually made outside the JB to a segment that entered the JB, appropriate data merger would take place automatically, retaining the segment # for the portion of the segment entering the JB and assigning a new number to the portion that has been created by the cutting.