It was established earlier in the season that Lucy and Amy had different fathers, which is why only Amy ceased to exist.
To set up Wyatt's line about a man with an Eastern European accent identifying communist spies to McCarthy, the script has McCarthy asking Flynn, earlier when he's in his office, where his accent is from, even though the previous 11 episodes make no mention of Flynn's supposed accent.
When talking to Senator Joe McCarthy, Wyatt mentions Flynn's "Eastern European accent". Flynn is a multi-generation American and is not supposed to have an accent. However Goran Visnjic, who plays him, being Croatian-born, does.