dropped/disregarded dice are not counted towards dice sums, though I am not familiar with Wretched and Alone mechanics - if you need to completely remove a certain kind of dice from a pool so that they aren’t included in re-rolls, you will need to do that manually for each individual die (though it may be simpler to just have an expression that counts the 1s, and then you can roll a pool with that many fewer dice next time).
I hope that helps!