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:
https://skyline.ms/files.url

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.
-- Nick

Dear Nick,

I did indeed use the Peak Boundaries import. So I think that is a great clue.
I am attaching the "Peak Boundaries.csv" that I imported.

The Peak Boundaries.csv was actually also created with the same skyline document. The reason I am doing this workflow of exporting boundaries and reimporting them has to do with the long standing issue of transition areas not being recalculated on reimport of results.
I had reported this earlier (https://skyline.ms/announcements/home/support/thread.view?rowId=52333) and you thankfully responded and worked out some fixes but eventually it didn't completely resolve my issues.
Ever since, I have frequently been adjusting to e.g. use additional transitions and then to get all peaks to update, I was exporting "Peak Boundaries" and then importing those right away. This was a very effective fix for me.

Comparing to some other peak boundaries files, I think they always had the same format. So the recent change would then likely have to do with how the import works.

Best,
Jonas

I also just realized the Peak Boundaries I uploaded are from the complete document as opposed to the minimal example that I uploaded earlier. I think that won't affect the conclusions though.