Assuming the child object name as `ChildObjectName__c` and lookup API name on child is`LookupName__c`, your query with where clause would look as:

    SELECT  Id,
        (SELECT Checkbox__c FROM ChildRelationshipName__r)
    FROM Parent__c WHERE Id IN (SELECT LookupName__c FROM ChildObjectName__c)`

Related documentation for reference: [Basic SOQL Relationship Queries](https://developer.salesforce.com/blogs/developer-relations/2013/05/basic-soql-relationship-queries.html)