I ended up with a working directory where <tt>fossil changes</tt> says:
<verbatim>
Index: env-msvc.cmd
===================================================================
--- env-msvc.cmd
+++ env-msvc.cmd

Index:
===================================================================
........
</verbatim>

For me it means something like there are no changes, but I don't know why it gets listed in the diff. And trying to commit all files but 'env-msvc.cmd' (specifying the files manually as 'fossil commit' arguments), gave me this error AFTER typing the commit message, no matter how many times I try to commit:
<verbatim>
New_Version:
fossil: tree checksum does not match manifest after commit: versus
</verbatim>

About how I reached that state...
I had a tree of changes. Then I did: <tt>fossil merge --cherrypick XXX</tt>

That brought a little change in <tt>env-msvc.cmd</tt>.

I then did <tt>fossil revert<tt>.

That said to have reverted all the changes I had.

Then I did <tt>fossil undo</tt>.

That brought the changes back. I did not want the change that got merged in the file for the cherrypick, so I did <tt>fossil revert env-msvc.cmd</tt>.

And then it still appears in the diff without changes shown. As a clue, I'm on linux, and the env-msvc.cmd has CRLF line endings (it's mostly to be used on windows).