(asked somewhere else a while ago but haven't reported here...)
When you play Replace to gain a Border Village to your discard pile and gain by its on-gain effect a card covering it up, Replace, my guess, should lose track of and fail to topdeck it despite of successfully checking its type, shouldn't?
The current implementation is the opposite. Now Replace also topdecks...
the gained Cache covered up by Coppers.
the gained Death Cart covered up by Ruins.
the gained Skulk covered up by a Gold.
the gained Cursed Village after it is covered up by cards you discard or gain when you resolve particular Hexes.
Of course events such as Watchtower+Border Village work correctly, so Replace matters.
Again, thanks for reporting this issue and I can confirm all the problems you mentioned. Replace (like Watchtower) should loose track of the gained card if it is covered up.