In terms of thinking of MTG I tend to think of buffs as enchantments. When the character leaves play, the enchantments leave too.
In terms of thinking about RPGs I'm thinking of gear or levels. That leaves 2 ways of thinking of this. 1 is when they leave play and come back they are as they were (they took their toys and experience with them and had it when they came back). The other is that they lost their equipment (in this case it would be buffs from other cards. For example, they would lose their wings from Angelify) but keep their "levels" (in this case Agent Coyle Mechborn would keep his self increased stats).
Since all 3 options can be justified to some extent, it seems that the best solution is the easiest. Unless something specifically says it retains bonuses when coming back to play, it loses them. This also leaves open the possibility eventually for cards that do retain their bonuses and/or do leave play like Pilgrimage Monk in the future. Maybe a mechanic similar to phasing from MTG or something like that. So it is a simpler mechanic and offers other options for the future.