etcupdate created empty files = system unbootable

Yesterday I upgraded one machine from 12.3 to 13.2 with source upgrade 
(installkernel & installworld).
Then I run "etcupdate" (about 100 changes listed, mainly U and A, only 2 
C), "etcupdate resolve" to solve conflicts in newsyslog.conf and 
sshd_config, then "etcupdate status" to be sure everything is OK, it 
just said: "Modified regular file remains: /etc/motd"

After this I updated bootcode with gpart and rebooted the machine but it 
does not come up, cannot login via ssh. Accessing this remote machine 
with remote mamagement / IPMI was a nightmare. It took me almost 5 hours 
because of java etc. but it's a different story.

The machine in question is all ZFS based. I did similar  kind of upgrade 
many times but this time the etcupdate left more than 80 files in /etc/ 
empty. Almost all files marked as U (updated) or A (added) by the first 
run of etcupdate was empty. So there were non functional files in 
/etc/rc.d/, empty /etc/login.conf and many more which means the system 
cannot boot to multi user. I must boot into single user, restored files 
from snapshot before upgrade and then it booted.

Question number 1: How etcupdate can go so horribly wrong to put empty 
files in /etc/ and make system unbootable?

Question number 2: What's the right way to fix this with etcupdate now?

# etcupdate
Failed to build new tree.

I don't know if I am alone but I definitely have more problems with 
etcupdate in a few years of usage instead on mergemaster. I don't 
remember so many errors, unhandled automatic updates or syntax errors in 
important files with mergmeaster in about 15 years.

Kind regards
Miroslav Lachman