I know, I should only change files in a project, when the repository is opened. But I now tried to see what happens when I change a file when the repo is closed, because I will often do that, because I'm going to forget to open repos. It's inconvenient ...
Now I see what happens: changes are not recognised. Doing a commit, I get the message "nothing has changed" ... which is not true.
What can I do to make fossil recognise missed changes?
Why did you close the repository? When you do fossil open, fossil will try to deploy the latest version. Maybe it has overwritten your files…
You should use open .... --keep if you don't want to harm your working directory.
As a comparison with git (seems that it's your background):
.git folder. Multiple working directories for the same repository are typically hardlinked._FOSSIL_ or maybe .fossil depending on your version. It contains both a pointer to the repository (the object database) plus workingdir-specific data (what you'd call HEAD, stash, uncommitted additions/deletions/renames). close will delete that file. So, in git terms, it's like if you did git clone --bare . some_other_folder.git and then recursive rmdir .git. You still have the project history somewhere, but all information about your working tree is lost.