Can you send us your Skyline document and also zip up your raw file "EAM0021_CnF1T_V8AmBic_1-C,2_01_3712.d" and send it to us?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.
Please send us that .sky.zip file as well the zipped up folder "EAM0021_CnF1T_V8AmBic_1-C,2_01_3712.d".
You can upload those files here:
When Skyline is extracting chromatograms, Skyline writes data out to a bunch of temporary files before everything eventually gets put into the .skyd file. The error that you are seeing is happening because one of the temporary files ended up being more than 2GB in size, and our code cannot handle it.
Skyline is supposed to choose how many chromatograms can fit into each temporary file, based on the number of scans in your raw file, so it's not supposed to be possible for the error that you are seeing to happen.
It sounds like there is an error in Skyline's estimate of how many points some chromatograms are going to have. After we see your files I imagine it will be straightforward for us to fix this.
Thanks for reporting this issue,