CJ,
equipment and Floc CT table will always have heavy amount of records. Reducing entries of these tables is little tricky. And i don't think you can achieve it what have mentioned by manual sync.
In my case, I have handled this scenario in different ways.
1. Disabled these tables means don't download these tables to the client at all. If technician will create work order/ notification from selected order then copy the equipment/floc from selected order/notification.
2. Removing unnecessary indexes in Agentry client will make sync process little bit faster.