First, Switzerland is not "pulling out of Schengen". Brussels has threatened it in retaliation for a Swiss vote it didn't like, but Brussels says lots of things. There are many ways this could play out.
Second, Switzerland has only been in Schengen for around 5 years. CERN has been around an order of magnitude longer.
Third, the most immediate affect will be to make crossing the Route de Meyrin between ATLAS and CERN a lot easier and safer, since there will be huge backups at the border and cars will be moving more slowly.