Uncle Henrik really is happy that Annemarie has gotten there. And he is happy that the dogs smelled the handkerchief, but he does not really care that he actuall has gotten the package. I think that he is not just being polite, but he is not really thanking her for the package. Instead, he is thanking her for what she has done in bringing it.
We are told that the handkerchief was important because it ruined the dogs' sense of smell. Now the dogs will not be able to sniff out the people that are smuggled on to the boats. This means it was very important for the dogs to smell the handkerchief, but not really important for it to get to Henrik afterwards.
In the book "Number the Stars" Uncle Henrik had held a fake wake in his home for a non-existent Aunt Bertie. The scene was staged so that he could allow the Jewish families to gather at his home. They had gathered at the home and the soldiers came into the house. They wondered why the casket was closed and were going to have it opened. Annemarie's mother makes up a lie about the woman having typhus and she gets slapped by the soldier.
The soldiers leave and the rest of the plan falls into place. Uncle Henrik, who is a fisherman and has a boat, is going to transport the Jewish people by boat to Sweden. It is very dangerous. Everyone leaves as planned.
However, the mother had found a package that peter had said was very important for Uncle Henrik. She had tried to take it to him but had hurt her leg. She had crawled back to the house. She has to have her daughter help get the package to him. It is very dangerous but the Uncle needs the package.
Annemarie hides the package under some lunch and heads through the woods to take it to her uncle. When she arrives at her Uncle's side, he accepts the package which he had no longer needed.