Re-annotate Schematic after Layout

Sounds like you are failing to  back  annotate.  Do that before doing any forward annotation and you will be fine 

Hello. You are not stuck but forward annotating a board from capture can be confusing depending on your view !

When you create your schematic and then package it to a .brd file capture usually presents some defaults in the netlisting screen. Here is that screen

As you can see there is an output board file. You can choose the directory and .brd filename to your own liking. Upon Netlisting capture creates the netlist and packages the design into the board file. So in the case of the example above Design1.brd is an "Output File"

As your design progresses you may need to re-sequence your schematic symbol reference designator's etc. When you do this you have to then create a netlist again so as to forward annotate the Design1.brd file.
So there is a got ya here but at the expense of alot of writing give this a try. Choose in the netlist dialog the "Input Board File" to be the same as your Output board file and hit OK to netlist and forward annotate the board.

When you open your board file in Allegro you should see that your reference designator's have changed and you don't have to place symbols you had already placed before. If you happened to change the physical footprint assigned in the schematic to a symbol then you will have to place those new symbols but for a reference designator change only,  then no footprint will have to be placed.

FYI: When you get your board to where you want it to be it is a really good idea to save that board file and or also save it as a different name. That way if things go wrong you can get back to what you had.
 it is a good practice to always Forward Annotate from the Schematic to the Board as opposed to back annotating from the board to the schematic. Main thing on this is you always always want to have the schematic in sync with that board file.

Here is another thing that may be useful. In Allegro you can create a board as a template with things like a sheet border place outline and all your color settings. You can use that board file as your input board file for any new designs you create going forward. Usually I keep Allegro closed during netlisting !. Maybe give the above a try and see how it works...

All the best

Paul.