The tool by default checks for deletions on Salesforce for past 24 hours. This can be reduced so the tool queries for each hour or less, since the incremental runs would be scheduled to run very often say every 30 minutes or every hour.
The default property value is deleted.query.days=1 stored in system.properties file located at <>dbsync-cdmWEB-INFdbconf, the value can be changed to query deletions for past hour by setting it to 0.0416.