The easiest thing for you to do might be to use ProteoWizard MSConvert to create a .mzML file which has removed the chromatograms that you do not want.
That is, you would use the command line program "msconvert.exe" and the command line would include a --chromatogramFilter saying which chromatogram numbers to keep.
For instance, to remove the first ten chromatograms you would do something like:
msconvert.exe --chromatogramFilter "index 10-" myAgilentFile.d

You could use ProteoWizard SeeMS.exe to look at the file and see which chromatogram numbers you want to get rid of. Hopefully they are all next to each other, otherwise it would be more complicated to specify which indexes to keep.

A different thing that you could do would be to set the "Explicit Retention Time" on your molecules. Skyline will discard chromatograms whose time range does not overlap with the molecule's Explicit Retention Time. However, setting the Explicit Retention Time has other effects that you might not want such as that Skyline will always choose the peak which overlaps with the Explicit Retention Time regardless of how the peak scores on other criteria.
-- Nick

Hi,

Thank you for the response, I will try those ideas.

I also found another work around when collecting the data. In the method editor on MassHunter, we can un-select store data for time segment 1, and have store data selected to time segment 2. Then when we upload the data into skyline it reads the file correctly and works for our needs.