The WeBWorK administrator (the person who creates courses using the "admin course") should be able to login (as admin, using admin's password) to an orphaned course and change a password for a specified user.
In any event, a person with shell access to the server and suitable privileges on that server has the option of running the "newpassword" command (it is in webwork2/webwork/bin).
Read the commented code to see the syntax:
WeBWorK Main Forum
Automated password recovery
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