One further point that may be relevant.
Towards the end of work on the previous revision, the schematic was back-annotated with reference designators set by the layout tool to give the components numbers related to their locations on the board.
I'm not trying to back-annotate now, but these errors seem to be related to the back annotation process. There are several components that have been deleted in the new revision so this error may refer to one of those.
I have now found Technote MG245885 which is relates to these error messages.
The Technote states:
Usually this problem occurs when the Block and the underlying schematic share the same name.
We have also found cases where this is not the case
It then goes on to explain how to change sheet and block names.
I don't seem to have that issue (the blocks all have $xIy style names while the sheets have human readable names describing their content) and the technote doesn't offer any guidance on what to do if the names are different but you still get these errors.
I've tried supressing the errors in the advanced tab od the PCB interface but the assignment of references doesn't happen so I'm still stuck.
OK, this is very odd.
If I do File/Export/Cadence Allegro I get a netlist that corresponds to the schematic I have on the screen.
If I use the PCB interface (Generic Netlist configuration) a netlist is produced but it has devices that have been deleted from the schematic and the reference designators are the "old" ones from the previous revision before it was re-referenced by back-annotation from the schematic. The new devices don't get referenced either.
Where does this "stale" information come from?
OK, I think I've found it.
As part of a work-around in the previous revision, the design was itself added to the libraies in Setup/Projects/Symbol Libraries as instructed.
This provides an absolute link to the old revision which didn't update when the design was copied to a new location to do the work for the new revision.
I have removed the old library reference and added the new design in the same way.
This has cured the problem.
I hope someone finds this useful......