In the following years, Queen Margaret acquired large parts of Schleswig as security (Tønder fief, Frisland, episcopal manors in Svabsted and Stubbe) and by purchase (Trøjborg, Skinkelborg and Grødersby); King Erik took over Haderslev fief as security from the fiefholder Helene Ahlefeldt, and the queen, Flensborg.

However, in 1408, when Gottorp was about to be taken over by the Danish crown, Catherine Elisabeth called her son Henry back from Denmark and had a declaration of hostility sent to King Erik on 14 June 1410.

Several foreign princes, among them her brother Henry the Mild, Duke of Brunswick-Lüneburg, tried to intervene and mediate but without lasting peace.

In 1415, her son Henry was declared of legal majority, the reign of Catherine Elisabeth ended and she is no longer mentioned much in the documents.

In 1423, her sons submitted a complaint that their mother had been assaulted by the royal soldiers despite the promise that she was to be left out of the conflict: her carriage had been attacked and her male staff had been mugged and captured.