In the Q&A style of stack exchange, I had this error and couldn't find a solution.
The accident was cause by me typing:
fossil update a_filename
This leads to corruption of the fossil-scm settings which outputs:
SQLITE_NOTADB: file is not a database
D:\bin\fossil.exe
SQLITE_NOTADB: file is not a database
D:\bin\fossil.exe: file is not a database
PRAGMA database_list
SQLITE_NOTADB: file is not a database
D:\bin\fossil.exe: file is not a database
PRAGMA database_list
SQLITE_NOTADB: file is not a database
D:\bin\fossil.exe: file is not a database
PRAGMASQLITE_NOTADB: file is not a database
^C^C
This runs forever.
The solution to this problem is to re-sync:
fossil sync https://<my_username>@<url>
which will prompt for password and deliver a status message that everything is okay.