Compare the amount of data in the tables involved. Perhaps someone did some inserts or deletes that changed estimated row counts.

Verify that the queries are EXACTLY the same, and I do mean EXACT. If views or functions are involved, verify them down to the character as well.

Verify the actual schema of all tables involved. Someone could have changed a column from a varchar(20) to an Nvarchar(20).

Check data value distributions. Someone could have updated data which caused estimated rows to vary between the two database copies.