on vcenter server are stored distributed switches configurations, host profiles, historical performance data and etc.
you can make a fresh install of vCenter Server and migrate all esxi host there but you must carefully plan each step.
my recomendation will be to make an upgrad like it is described here: VMware KB: Upgrading vCenter Server Appliance 5.0.x/5.1 to 5.5 and solve post upgrade issues if they appear. fresh install, always must be last option.