This would be the reason... Cross-class and other unavailable skills at the level you're syncing to.
Let's say you're a SCH, AST, ACN or PLD (Cross-class Stoneskin), when you level down to level 10 that skill may be in a cross-class slot which is no longer available to you at that level. Also as a WHM/CNJ, you wouldn't have learned Stoneskin yet so at that level you shouldn't be able to benefit from it. In order to keep this from happening they need to remove the buffs you no longer should have access to, but to dynamically go through all of your buffs and compare them to your cross-class slots or your class/job abilities would be a sizeable drain on resources. To solve this and make it as resource neutral as possible it's just easier to remove all of your buffs entirely.