Well, I've been a bit dull. Of course I have not seen any nags - I have disable-dso installed on all three machines! They all still work fine, regardless of the LCN shuffle, although I have had the Freeview info pop-up (press yellow to cancel) which I suspect is triggered by the Freeview virtual machine detecting a disparity between the broadcast LCN and the LCN stored locally (does anybody get these messages once they have retuned?). I reckon there might be an opportunity to reassign the LCNs by database manipulation instead of a retune faf - which is not the same as channel renumbering.
I have retuned a TV and confirm the LCN shuffle has taken place.
Anybody on 1.02.27+ and relying on disable-dso should note there is a slight chance the retune can still get through - the EPG refresh wake-up presents a small window of opportunity within which the DSO event can get scheduled and acted on before the custom firmware can intervene. The same applies to other times the box is on but not attended (to opt out), but the EPG refresh is more critical because that is necessary to ensure series get recorded while you are away for a period.