Counters disappearing in Library

[Halfmind]

Hello all!

I was wondering if anyone could help me out with the following:

The game I am creating has cards that add an affect to a card before shuffling it back into your deck.  To manage this, I've simply been adding a counter to said card, then shuffling it into the deck.  The problem is that it seems sometimes the counter persists, and sometimes it doesn't!  Does anyone have any information on this?  Thank you in advance, and have a wonderful day!

[Trevor]

There is a preference to automatically clear cards as they are moved off the table.

[Halfmind]

Unfortunately, when a card is placed into your Library, it is still cleared even though the preference is unchecked.  I've tried this multiple times to make sure it is consistent, and it is.

[Trevor]

If I recall correctly, moving a card to a concealed zone will clear the card, or at least hide any counters it has on it until that card is revealed. With physical cards, you just can't have counters on cards while they are in a pile of other cards, so Lackey tries to emulate that.