I made a test 2.5 quest. When I continue, the correct percentage of hearts are filled. In a 2.10 quest (namely, mine), Link always continues with three hearts, though I have the Continue HP set to 75%.
I don't know about quests that are <2.10.
[743] 2.5 doesn't recognize 2.10 quests' Continue HP
Does this bug only occur if you access Link Data in the cheat menu? If so, it's fixed in the next build.