We're working on this, but for now here's a workaround:
Open the .sky file in any text editor and find the line containing
and change that to
This changes the Full Scan MS1 filtering Resolving power, which changes Skyline's idea of which calculated precursor isotopes are viable. Skyline is applying a test on file read that it didn't seem to have applied when the file was being created, and one or more M+1 isotopes are being rejected as being inconsistent with the settings. We're looking into that, but it comes down to we should always read what we write.