On 18/09/2012, at 4:08, Julian Bogdani <jbogd...@gmail.com> wrote:

> Hello
> I've posted a question on gis.stackexchange.com 
> (http://gis.stackexchange.com/questions/33608/layers-in-qgs-file-not-present-in-the-layers-pane),
>  and as promised there I'm sending here a qgis project file with a phantom 
> layer to use for test.

[snip]

> As you can see in the same file other traces of older files are still present 
> in the xml, for instance near lines126 and following: a list of vector layer 
> with snapping turned on. This does not produce any error, but getting them 
> removed when layer is removed is probably cleaner.

As a you're not hallucinating comment (rather than a solution) I also have seen 
such things, although I'm not sure I have an example to hand. 

Is it just in projects saved by QGIS 1.8?

I think from memory mine are with relative paths, and are projects originally 
started under an earlier QGIS version. 

Save As did not work for me either. 

-ramon. 
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