Hi Hans,
We recently changed the behavior on scores from PD, so depending on which version of Skyline/BiblioSpec you are using it may differ. Most recently, we are filtering based on the TargetPeptideGroups.Confidence column if you use a score threshold of 0.01 (corresponding to confidence 3) or 0.05 (confidence 2). In these cases, scores will be unavailable like you noticed. Otherwise, we check for various columns: (in order of preference) Qvalityqvalue, PercolatorqValue, qValue, ExpectationValue.
The SpecIDinFile is based on the workflow ID from PD like you mentioned, and also the spectrum ID. I'm not sure how PD assigns spectrum IDs, but you can find them in the MSnSpectrumInfo.SpectrumID or MassSpectrumItems.ID columns.
Thanks,
Kaipo