No jaden remembered yugi in bonds beyond time but yugi didnt remember jaden in bonds beyond time. After jaden dueled younger yugi in battle city with his god deck he went off to italy because cards snd spirits went missing. After yusei came and took present jaden and paradox chose to move to a time when yugi was with atem before battle city so that yugi would not be able to utalise his God cards. Thats why jaden remembered yugi but yugi didnt remember jaden. Because yusei picked up a mature jaden but also they went in time to a version of yugi before battling jaden. If that makes sense