That error is usually caused by a bug in Skyline where Skyline is now calculating a different m/z value from the molecule than when Skyline saved out the document.
Sometimes this happens because of the way that the molecule was inserted into the document, and changes were later made to the molecule, and the way that Skyline ended up applying those changes caused Skyline to calculate a different mass than if Skyline were to calculate everything again from scratch.
If you send us your .sky file, we can send you back a fixed version of that file which you will be able to open without error. After that, we might have some follow up questions to try to figure out why Skyline was making this mistake.
If your .sky file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here: