Subscription/Publisher data are deleted abnormally

We've got a merge replication. I have one Publisher and one Subscriber. I've made a pull subscription to a Publisher.

Publisher and subscriber are working fine far more than one year, Recently I got issue at subscriber one table deleted for 3 rows, I take usually and think it was never happen in this system, that will not be in future, yesterday again one row deleted from another table at subscriber, so I think it is serious issue and look over the details, I found following-

The process could not make a generation at the 'Subscriber'.
The process could not enumerate changes at the 'Publisher'.

Error code -2147200994

Which parameter of the subscription is responsible for it?

I Found data deleted by ‘System delete’ also, Why it is happening we don’t have any clue. How we can rely on the Sql Server.

We are using SQL Server 2000 with Service pack 3. Can we upgrade with SP4, is there any possibility of improvement in the same.

Each clue is too valuable for us. Can any body have experience on the same?