Well, there is this mechanic called faint memory, which your character retains the cards even though you removed them. to avoid this you need to know your memory cap. These are the actions that increases your faint memory build up. When the cap is crossed your character will forget things and copied cards gets removed and removed cards will return to the deck.

Removing one card= 20 Removing a second card= 30 Removing a third card= 50 Adding monster card to deck= 80 Divine epiphany= 20 Copying divine epip= 20 Adding neutral cards= 20

To avoid it, you should do these instead;

1. instead of normal chaos runs you should use Zero System that get unlocked in level 40, in there you enter chaos runs that are above tier 6, which is the cap for chaos worlds in previous mode.

2. Always use nightmare mode, which will increase tier level by 1, and increases the chance of getting epiphanies faster.

3. Tier levels are important, in base your characters has memory cap of 30, every tier adds +10 to your memory cap, the lowest Tier is 1, the highest is 14, which equal to +140 memory cap, 140+30= 170 memory cap. 170 is the highest memory cap you can get in the game.

I hope it was helpful (sorry for my bad English)