It appears that you are using Skyline version 21.2.
The current version of Skyline is 23.1.
We usually recommend that you use the latest version of Skyline unless you are trying to reproduce results from older experiments.
We have fixed some bugs in older versions of Skyline which were causing problems when the .skyd file (the file which contains extracted chromatograms) became very large.
It is likely that Skyline 23.1 will have fixed the problems that you are running into.
If you are still having problems with Skyline 23.1, then it would be helpful if you could send us your Skyline document and some of your raw files.
The usual way to send a Skyline document is to use the 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. It will probably be much larger than that so you would need to upload it here:
https://skyline.ms/files.url
It would also be helpful if you could send us some of your .raw files that you are trying to extract chromatograms from.
However, it is very likely that the problems you are running into will be fixed if you use Skyline 23.1 or Skyline-daily instead of Skyline 21.2.
-- Nick