If you run on CRM server version 2013 SP1 or later, you can use the advantage of the linked filters, that will work not only on initial/full synchronization, but also on incremental synchronization. If not, from the incremental synchronization definition, only records, that are changed will be included.

To create a linked filter, you just need to add a link to the associated entity. In this example I want to synchronize only Opportunities that are associated with account records owned by the user.

So I create a synchronization filter like this

If you are running CRM 2011 or CRM 2013 (without Service Pack), this filter will work only at full synchronization.

Next step to make the filter work on CRM 2013 SP1 and above also at incremental synchronization, you need to do is to enable the use of “Incremental Linked Sync Filter” for the entity

It can be enabled by default in the project’s Configuration, but it is not recommended as such filter will create a complex query, that might increase server load. So we recommend to enable this option on per entity basis.