Unfortunately have already been through that KB article, it is not very useful for ESXi 5.
e.g. one of the first steps it mentions is running:
[root@esx-server /]# cat `ls -t /var/log/vmware/vpx/vpxa*` | head -1
However, vpxa logs have been merged with hostd.log file in ESXi 5 from what I can gather. Also, the KB articles that it links to with instructions for re-installing the vpxa agent, also mentions that the vpxa agent cannot be reinstalled for ESXi 5 as it is part of the esx-base package.
So I am wondering, what is the best practice here in ESXi 5? I was hoping there was a better solution than bringing the host offline and performing a fresh install, reconfiguration, etc.