synchronizing local and server database
Replication, and daily / hourly backups (depending on your need), probably with something like xtrabackup, and storing the binlogs in between, give your pretty good point-in-time recovery. You might even configure pt-slave-delay to let your actual backup lag somewhat, useful for those moments where you are aware of an accidental deletion within the time-frame of your delay, making the restoration a bit less cumbersome.

I do not understand the requirement 'all features should be done by using billing software'. Billing software is for billing, not for database maintenance.