This isn't really a ZF question but more of a system design question. There are a number of ways to solve your problem if you data isn't ordered you can use such as bulk transfer, timestamp and math based or if its ordered you can use revisions to sync data.
Doing the synchronisation using transactions, so that if any of the commits fail the system is rolled back, will prevent the issue of partial data sync, this gets more complicated when the data sync is 2-way but isn't an impossible problem to solve. Things to consider whilst building or refactoring is 1. How up to date does the data need to be 2. What and where will conflict occur 3. What level of accuracy do I need to maintain 4. Are there any referential integrity issues I would suggest you do some research on data synchronisation strategies via your favorite search engine and then decide the best way forward for your solution. Regards Marco
