Why may I have to enter a second factor (e.g. TAN) for manual synchronisations, although the 90 days have not yet expired?

The intervals at which strong customer authentication is required depend on your bank. Many banks require strong customer authentication every 90 days, while some banks require strong customer authentication on a case-by-case basis and others with each account access. See also category > 5. Regulation and financial supervision, the question: What is strong customer authentication?