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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_F__.xml:114: parser error : expected '>'
</N
   ^

It seems like the problem is in row 114 with a missing '>'. Lets check the xml file

OMD[mysite]:sed -n '2p; 114p' var/pnp4nagios/perfdata/MYHOST/Filesystem_F__.xml 
<NAGIOS>
</N

And here we go. Row 114 seems to be uncomplete.
Please add "</NAGIOSNAGIOS>" and save the file.

The file should now look like this:

OMD[mysite]:~$ sed -n '2p; 114p' var/pnp4nagios/perfdata/MYHOST/Filesystem_F__.xml 
<NAGIOS>
</NAGIOSNAGIOS>

If you now run cmk-update-config -vv --debug again, there should be no error