Hi Kendra,
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
precursor_res="120000"
and change that to
precursor_res="60000"
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.
Cheers
Brian