Currently, the patron import tool allows a user to replace passwords. However, this does not overwrite passwords for patron categories using the "Staff" category type. While this is an understandable security measure, it doesn't appear to be stated in documentation which can lead to confusion about why it sometimes "works" and sometimes doesn't.
See Bug 41777 for a related enhancement.
Relevant section: https://koha-community.org/manual/latest/en/html/tools.html#patron-import At the same time as adding this information, it would be good to update the screenshots and review all the notes in that section.