Are you saying that you did:
File > Export > Isolation List
and you are getting some peptides that have been deleted from the Targets tree?
That does not seem possible to me (although I am not that familiar with exporting isolation lists, so there might be something going on that I do not understand).
It might help if you send us your Skyline document.
In Skyline, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral libraries.
If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
By the way, when you delete the peptides from the Targets tree, those peptides will still be present in the spectral library. That is, you will still see the peptides:
View > Spectral Libraries
If you would like to remove those peptides from the spectral library, you can do:
File > Share
and on the "Share Skyline Document" dialog choose "Minimize Libraries". This will remove all peptides from the spectral library which are not present in the Targets tree.
If you then open the .sky.zip file, you will have a document whose library does not contain the peptides that you deleted.
However, those peptides not being in the spectral library should not have any effect on the isolation list you are exporting.