Hi,
What you do is the following:
1. Create a netlist of your current schematic and load it into your PCB. (make sure the "device/net/pin name char limit" is set to 255 in the 'setup' menu of the "create netlist" window)
2. in Capture, go to the Annotate menu and select 'Unconditional reference update'. Also tick the 'REFDES control required' box. In the table which becomes visible choose your start and end value so that ALL refdesses are to be new ( nothing that will be assigned can be already in the current design.) so for instance Start value 10000 and end value 20000.
3. i'm not fully sure about this step, but i always use it when i have to perform this task: enable the box "Preserve designator"
4. create a netlist of this newly annotated schematic and load it in the PCB. no components should be removed from the board
5. now go to your schematic and do a new annotation of all refdesses the way you like. (make sure NO refdesses are reused from the range earlier specified (10000 to 20000 in this case)
6. create netlist and load in the PCB. >> done
Allegro tries to match new/changed components to the pcb based on REFDES. by doing it like above we force allegro to other methods of matching. (some internal referencing)
Greetings!