You can only combine Profiles in FIMS.  If you combine profiles in FIMS, and choose to delete the FROM profile (which is an option in the Combine Two Profiles utility), all the FIMS-related data will move to the surviving profile.  Once the sync is done, if there are any FIMS CRM-specific records such as Opportunities, Notes, or Event/Campaign records, those will be lost from the FROM profile in CRM.  So care must be taken when deleting or merging profiles. 

We recommend that security be set on the Combine Two Profiles utility in FIMS so only those who understand the ramifications for FIMS CRM be able to do this.  Anyone who is going to delete or combine profiles should check FIMS CRM for data that may be lost and move it to the surviving profile before the combine is done in FIMS.