I am not sure that I understand your question.

Are you asking how to adjust the peak boundaries for one particular transition, and leave the peak boundaries for the other transitions within the same peptide or molecule unchanged? It is possible to do this in Skyline.
If you select a Transition in the Targets tree, and then right-click on the chromatogram graph and choose "Transitions > Single" then you will be looking at just the chromatogram for that one transition. If you then adjust the peak boundaries, the peak boundary change will only be applied to the single transition that you are looking at.
We purposely made adjusting the peak boundaries for a single transition require these extra steps because it's usually not what you would want to do.

Does that answer your question?
If your question was about something else, it might be helpful if you could send us a screenshot of what you are looking at or send us your Skyline document.

To send us your Skyline document, you can use the Skyline menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick