It is actually very easy to renumber features. This can be very useful if you have added a new feature at a later stage and want to keep the features listed with say habitat features first followed by species features or whatever.
To do this, you first open each feature in turn and see what numbers they have. Then if your feature number 9 has to become number 5, open each feature from 5 on and change the number to 25, 26, 27 etc or something. Then rename 9 to 5, 25 to 6 etc and then you have your features renumbered.
Factors, Management Aims and Attributes are slightly more complicated. It is probably easiest to delete all the Factors, Management Aims and Attributes, then recreate them in the order that you desire and finally reattach the projects.
When you delete the Factors, Management Aims and Attributes, the associated projects are not deleted but become unplanned projects. To reattach them, create the new Factors, Management Aims or Attributes, click the "+" on the project list and in the Select Project Code window, it is the first option "Existing projects for planning unit" that you need. It would of course be advisable to take a note of which projects attach to which Management Aim etc before you do this.