When you do /ce, click on the Alchemist and it will allow you to combine CE's. Custom enchants do not stay on SVA's after reset.
I'm a survival player and I thought they did stay on when the resets happen? Strange.
Also, you need to drag click (drop) the magic dust on the custom enchantment. No anvils, just drag drop them. Same with applying the enchantments to the book, drag drop it onto the weapon/armour your trying to apply it too.
Also, you need to have the same success level on each enchantment that you're trying to combine, for it to work. You also can't exceed a certain success level aswell. Or it just won't combine for same odd reason.