My Rx for core replacement ....
Suggestion is to cut the minimum amount of the top FRG layer ... so you can correctly taper (12:1) the replacement FRG layer TO the 'margins' of the old FRG decking. During the demolition process you can leave athwartship 'strips' as temporary 'benchmarks or guides' so that you keep the top deck profile straight and level.
For core removal, I use a circular saw to cut through the 'wood' with enough kerfs to affect loosening them ... followed by the use of an air chisel to make quick work of the core removal. If you 'prefer' to hand chisel out the core, prepare for some agonizing and backbreaking work with a sharp cold chisel and hammer. Then, grind the bottom FRG layer smooth, trying NOT to remove too much so you dont affect the structural integrity of the bottom FRG layer.
New core can be balsa, or Klegecel, etc. applied over an epoxy 'mush' and the vertical joints also 'mushed'.
Do all your 'leveling' for the final FRG layer ON the new core, grind/sand as needed.
Use 'heavy weight' glass cloth to minimize the 'number of layers' applied and overlap the edges onto the beveled 12:1 taper that you ground/sanded on the remnants of the OEM 'top layer' of FRG. Then with a belt sander taper the overlaying new FRG FLAT to create the 'taper' match to what you originally ground/sanded in the OEM deck. 12:1 is needed to restore 'structural integrity' to the top layer of FRG. Use epoxy 'mush' to level the core before applying the final FRG cloth and resin layers. If you get the top surface of the core flat and level, the application of the top FRG layer will go 'smooth' and will require the least amount of 'filling and leveling' with 'mush', etc.
For the final surface consider to use already molded textured 'deck pattern' sheets ... basket weave, or 'stippeled' etc. and apply with epoxy 'mush'.
Spray color matched gel coat, etc. to hide the scars made in the exposed borders of the OEM deck etc. .... you really dont want to 'paint' the margins of the remaining FRG layer. If you plan ahead such spray gelcoat, can be minimized ... so you can use 'self-contained' PREVAL spray bottles for the gel application.
Hope this helps. Major re-coring of a deck is a nasty, back-breaking job.