When you got that error message, was there a "More Info" button? If so, could you press it, and copy the whole text of the message box for us? The "More Info" button if it is there will reveal information about where exactly in the Skyline code the problem is happening.
Skyline message boxes usually have a copy button located in the lower left corner of the message box which copies the full text of the message, including the callstack information from the More Info.
If there isn't a More Info button then we might have to tell you to send us your entire Skyline document. Usually we tell you to do that by using the menu item "File > Share" to create a .zip file containing your Skyline document and supporting files including spectral libraries and extracted chromatograms. However, from the error that you are seeing, it seems likely that "File > Share" will not work either. In that case, we may have to ask you to zip up all of the files that are in the same folder as your .sky file, and we will see if we will be able to figure out what is going on.
For now though, let us know whether there is a "More Info" button on that message box, and we'll figure out what to do next.