I've done some experiments, and, indeed, there is an issue with the whole-project outline when a new project is loaded.  It would appear that files no longer in the project are not being properly purged from the outline tree.  Your solution, switching to single file, then back to whole-project mode, does clear up the old project files because it does a complete purge of the outline tree in the process.  Good catch, and I'll start looking into a fix.  Sometimes such added complexity brings along some subtle issues that may not have been flushed out during testing.

There is a good chance that the project hasn't finished indexing under these circumstances.  The Fortran parser (and all the other parsers, incidentally) run relatively slowly as a background process.  The project outline will not be available, or possibly only partially available, until indexing operations have been completed.  Even on small projects, this process can take some time.  While there should be some better indication that work is ongoing, there currently isn't. 

I'll look into the issue further, though.  I'm not sure why pressing the refresh button is not triggering the current outline to at least clear, although the refresh is dependent on pending work indexing files being completed.

1. Open a recent project with many files.
2. Select file outline, project tab.
3. Open a recent project with few files.
4. Leave file outline, project tab still selected.

It doesn't update.

5. Click the circular arrow 'update' icon.

It seems still not to update.  IS THIS INTENDED?

6. Select file outline, file tab.
7. Select file outline, project tab.

Now it updates.
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John