What is left behind after uninstalling?

Uninstalling a CFEngine package does not remove any user data. Most data including the host identity ($(sys.workdir)/ppkeys/localhost.{pub,priv}), state, policy, and logs remain.

To completely remove CFEngine delete $(sys.workdir) typically /var/cfengine or C:\Program Files\Cfengine after uninstalling the package.

Should I delete anything if I am re-installing?

You may want to wipe $(sys.statedir) and $(sys.workdir)/outputs for a fresh start to log data and history.

You may want to revoke trust of other hosts by deleting $(sys.workdir)/ppkeys/*.pub ( excluding localhost.pub ).

Only delete the host identity if you want to generate a new key pair and establish a new identity for this host.