The usual reason that a protein might not get a fold change value is that all of the replicates had missing or truncated transition peak areas.
When Skyline is calculating the fold change for a particular protein, Skyline looks at the all of the transition peak areas in all of the replicates. If a particular replicate is missing the value for a particular transition peak area, but there is at least one other replicate that does have a value for that transition, then Skyline throws out that replicate. You can reduce the chance that there will be any transitions with missing areas if you check the checkbox that says "Use zero for missing peaks". (You can see that checkbox if you push the "Advanced" button in the "Edit Group Comparison" window).
When fold changes are being calculated at the protein level, replicates have to have the complete set of transition peak areas across all of the peptides. Since that's a larger set of transitions compared to when calculating at the peptide level, that makes it more likely that any particular replicate is going to have to be thrown out.
I hope this answers your question. If it did not answer your question, then you should send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here: