I switched from bottle conditioning to keg/bottle fill this past year. With the beers that I entered with the thought that they could win awards, I got awards every 1 in 5 with bottle conditioned, and every 1 in 6 with kegged.
HOWEVER, the comments I received on many non-award winners suggested that I lost carbonation in the keg/bottle process and that likely had some impact on a few not winning awards.
Moral of the story: if you make good beer, it will win no matter how you carbonate it. AND if you change your process, it will likely take you a while to learn how to master the new proces and it may imact your beer in the short term.
I would say enter the beer either way. Getting the judge's comments have really helped me dial in my beers to be better!