>
> We have to mail servers running qmail + vpopmail 5.3.9
> The second server should get the vpopmail/domains dir via NFS from the
> first one. It seems that just the first 100 domains are working. All
> domans inside domains/0/ or domains/1/ are not recognized by the second
> server. I guess this has something to do with domains/.dir-control?
>

No, you must syncronize 
/var/qmail/control/rcpthosts
/var/qmail/control/morercpthosts
/var/qmail/control/virtualdomains
/var/qmail/users/assign

From the first server to the second server (better with rsync), then execute

/var/qmail/bin/qmail-newu
/var/qmail/bin/qmail-newu
/var/qmail/bin/qmail-newmrh
killall -HUP qmail-send

on the second server, to make it syncronize without restart qmail.

Regards.

-- 
Davide Giunchi

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