The most obvious explanation is that the file got corrupted between the last time you used it and now. Have you looked at character 1,025,795? I admit that is a pretty lousy error message. Not many text editors make it easy to jump to a specific character, but I just looked at EmEditor, our favorite text editor for large files and it at least tells you the byte index of the cursor. Though, it looks like you have to Go To a line and then check the byte index until you get to where you want.
Have you installed ProteoWizard and checked to see if you can open the file with SeeMS?
We would expect you to get the same error. This kind of error is generally indicative of a file corruption. It may be that you find it has been truncated at character 1,025,795, or just that something unexpected happened there.
If you would like us to have a look, you can ZIP and upload your mzXML file to our file drop point:
Thanks for using Skyline in your research.