So here is what I did to fix incredible big quota.user file:
Stop the quotas:
Delete quota files.
Create new quota files, build new one and turning quota on:
touch /quota.user /quota.group
chmod 600 /quota.*
Now my quota files has proper size:
# ls -lth /quota.*
-rw------- 1 root root 2.5M Nov 14 21:35 /quota.group
-rw------- 1 root root 2.5M Nov 14 21:35 /quota.user
Unfortunately quotas of all users seems to be gone so I have to rebuild them by manual changing quota in ispconfig. May be is better way to rebuild it .. I don't know it
For now everything seems quite well. Even differences between quotacheck and du -sh changed:
# du -sh /var/www/web16
# repquota -avugs |grep web16
web16 -- 726M 800M 801M 5986 0 0
web16 -- 0 800M 801M 0 0 0
.. not as I expected but better than before ..
may be somebody know what happend ..