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Hi Ranjith,
You need to use inner sub Query and perform your custom logic as per your requirement something like this :
for(Account acc : [SELECT Id, primary__c, (SELECT Id FROM Address__r ) FROM Account]){

if((acc.primary__c == TRUE) && (acc.Address__r.size() > 0)){
acc.primary__c == FALSE;
}

//Your custom logic
}

Thanks.