I had removed a file. Then issued a "fossil update", and the file was not in the list of files to be deleted on commit anymore.

I've had a session like this:
<verbatim>
$ fossil rm MERGE.txt
DELETED  MERGE.txt
$ fossil commit
...
fossil: would fork.  "update" first or use -f or --force.
$ fossil update
...
$ fossil commit
fossil: nothing has changed
</verbatim>

So I have to issue the <kbd>fossil rm MERGE.txt</kbd> again. The MERGE.txt file has not been touched in any commit other than this I planned to do.