Getting problem with downtimes are disappearing somtimes

I am really facing problem with downtimes. somtimes all downtimes for hosts are disappering and sending notifications. it is really pain to enter downtime again. is there any way to resolve this issue.

Are you restarting nagios and then you lose comments, downtime, etc or perhaps you have more than one nagios running?
/etc/rc.d/init.d/nagios stop
then make absolutely sure they are all stoppped.
ps -ef|grep nagios
then start it up, make your downtime settings, and you should be good till the next reset.

when i restart server downtimes are disappearing

Restarting the server or just nagios.
If you are restarting the server, then use a cronjob to take care of your scheduled downtime needs.
I use Sched Downtime via cron