This is a bit of an open ended question as it depends on just how much you are changing. By creating hierarchy you may cause some net renames to happen, it depends how ambitous you're being. In general, providing you stick to the same net names and same Reference Designators you ought to be OK. Just zip up the design at various stages as you change things, that way you can always step back. Have you looked at the in-line block creation to push sections into hierarchy? Use the Add Block command, fence the required area and use the Extract Schematic option - just bear in mind that you cannot easily undo this step (well you can only undo it manually). So experiment and see how it goes.
I have allways been confused by the net and component id ie $1Nxxxx & $1Pxxxx values and how they relate to packaging.
For the net to not rip up do I need to preserve the name or id property or both.
I've never done it, but if I only change a net name does it get ripped up?
My only experience with this is ORCAD, where if connectivity doesn't change, ie if R1pin 1 connects to R2 pin 1 before and after the ECO then ORCAD just renames the net in layout without ripping anything.
I had completely forgotten about the pushing sections into hierarchy feature which will probably do most of what I want to achieve.
The straight answer is I don't know whether the default names cause an issue, but generally net changes only cause a net to be trimmed back, it is the Ref Designator changes that cause things to be disconnected and thrown off the board. As I said earlier, do it one step at a time to get a feel for what effect your changes have on the layout.