Can you send us your Skyline document and your mass spec data file(s)?
I am not sure I understand your question but if I see your data it might make more sense.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
The Share Document dialog gives you the option of including your mass spec data files, or you could send those to us separately.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick

Thank you for sending your Skyline document by email. That particular address is not actively monitored, so it usually takes a few days for us to notice when mail arrives there.
It looks like you are using Skyline version 22.
We always recommend using the latest released version of Skyline unless you are trying to reproduce results in old experiments.
The current released version of Skyline is 25.1.

You can make multiple copies of the same molecule by selecting the molecule in the Targets tree, and then using the "Edit > Copy" and "Edit > Paste" menu items to get multiple copies of that molecule.
Then you can use the "Edit > Modify Molecule" menu item to change the Name and Explicit Retention Time values of the new molecules.

One thing that you should do before that is go to the "Instrument" tab at "Settings > Transition Settings" and change the "Min m/z" value to a smaller number.
Currently, that number is set to 50, but there are some transitions in the document with a smaller m/z than that. Those transitions will be deleted when you do the copy/paste so you should fix the min m/z first.

After you have added these new molecules you should reimport chromatograms using the "Reimport" button on "Edit > Manage Results".
-- Nick