If you add transitions to your Skyline document, you need to tell Skyline to extract the chromatograms again in order to see MS2 chromatograms for the new transitions. You can do that with the command:
Edit > Manage Results > Reimport
This is what you do for chromatograms which were extracted from full scan MS2 data.
If instead you have SRM data, then it usually is not necessary to do a reimport after adding transitions, since Skyline usually copies all of the available SRM chromatograms into your .skyd file. With SRM data, missing chromatograms are usually caused by there not being any matching SRM chromatogram in the raw (or .wiff) file. Sometimes with SRM data it is necessary to set the "Method match tolerance m/z" to a higher number. That number is at:
Settings > Transition Settings > Instrument
If neither of these things fix your problem, then you should send us your data.
In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
You can send us that .zip and one of your .wiff (and .wiff.scan) files.
If those files are less than 50MB, you can attach them to this support request.
Otherwise, you can upload them here:
(but, you probably just need to do a "reimport").