We can fix that file for you if you send it to us.
It usually requires us to change some of the numbers in the file so that they match what Skyline is expecting.

There have been some bugs in the past where, because of the way that settings changes were made, the m/z that Skyline thinks some transitions have are different than what they would be if Skyline were to cleanly calculate them from scratch, and, for this reason, you get that error message when you try to open it.

You only need to send us the file whose name ends in ".sky". We will then be able to send you back a fixed version of that file.
If that .sky 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

Thanks both, I appreciate the help.

Find attached.

Here's a fixed version of the file.
You should be able to save this overtop of your original file and everything should work.

It would be helpful if you could send us your entire Skyline document now that this is fixed, so we can try to figure out what went wrong in the first place.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including the audit log which will tell us what changes you made.

Please send us that .zip file.
Thanks,
-- Nick

Thanks again, everything is working.

I have attached the .zip file

Thank you for sending that Skyline document.
The audit log was very helpful.

It looks like the problem is with the "Modify Molecule" dialog.
If you use the Modify Molecule dialog to change the Monoisotopic Mass of the molecule, then the m/z of the Precursor itself will be changed to reflect the new mass, but the m/z of the precursor transition (which is one level lower in the Targets tree) will still have its old value.
If you were to then save the document once you are in this state then you would not be able to open the saved file.

Thanks for reporting this bug. We will try to fix it soon.
-- Nick