I do not know how your document got this way, but you can tell something has gone wrong if you create a Report in the Document Grid that includes the column called "Best Replicate".
(If you would like to learn more about the Document Grid you can look at the Custom Reports tutorial)
The "Best Replicate" column is supposed to tell you which replicate has the best scoring peak selected, but, as you can see from the attached screenshot, Skyline thinks that the best replicate is the last replicate. That replicate has an area is "#N/A" indicating that the peak was removed.
Do you have any idea how your document may have gotten this way? It looks like the peak boundaries might have been imported using perhaps the "File > Import > Peak Boundaries".
If you did import peak boundaries, could you send me the peak boundaries file CSV file that you imported?
Also, if you have a copy of your document as it existed before the peaks were removed, that would be helpful too.
Files which are less than 50MB can be attached to this support request. You can upload larger files here:
I think the problem is that when the peaks were removed, Skyline should have recomputed which was the "Best Replicate". As it was, when Skyline exported the spectral library, no spectrum in the .blib file was marked as the best replicate, which caused problems when Skyline wanted to show you the graph that is displayed in the Library Match window.