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In the first line of the cmk-update-config -vv --debug output there is already a hint to the corresponding host:

Loading autochecks from /omd/sites/mysite/var/check_mk/autochecks/MYHOST.mk

Please fetch that name and remove the .mk suffix. Now you have the Hostname. In my case it's MYHOST.

Now you can use xmllint to debug that:

OMD[mysite]:~$ xmllint  -noout --format var/pnp4nagios/perfdata/MYHOST/*xml
var/pnp4nagios/perfdata/MYHOST/Filesystem_E__.xml:1: parser error : Document is empty

^

It seems that there is one xml file with no correpsonding rrd file and this xml file is also empty. Please remove that file and run cmk-update-config -vv --debug again