Can you possibly give us your Skyline document with data removed? (using File > Share - Complete to create a .sky.zip file) And one of the problem raw data files where you can't get a chromatogram past 110 minutes?
If you can upload these two files to:
We can have a look and get a better understanding of what is going on. Even if we can just get a raw data file and the precursor m/z we can have a look at whether there are actually spectra that should match beyond 110 minutes, since the most obvious likely cause of what you are seeing is that somehow your mass spectrometer stopped collecting MS/MS spectra that match your precursor m/z at 115 minutes.
Have you tried having a look at your files using instrument vendor software (Xcalibur, Analyst, etc.) or the ProteoWizard tool SeeMS? Do you feel confident that there are matching spectra beyond 115 minutes?