Here you have to remember on things to disable the “My Site Cleanup Job” before resetting the Sync database, otherwise you run the risk of it deleting all the user profiles in the farm as we found out during a reset: http://technet.microsoft.com/en-us/library/ff681014.aspx#resetSync
User profile sync serves as a staging area for data, and the data in profile store and social databases is the data consumed by the user profile service. So if the right steps are followed, you should be able to reset the sync service and related databases, without harming the user profile data. Here are a set of suggested steps:
1) Login as farm account
2) Backup the User Profile DB and the User Profile Sync DB
3) Stop the SharePoint Timer service:
PS D:\> net stop sptimerv4
4) Delete the data in the Sync DB using the following PowerShell script:
PS D:\> Get-SPDatabase
5) Copy the GUID associated with the User Profile Sync DB in the command line below
PS D:\> $syncdb=Get-SPDatabase -Id
6) Execute these commands, in exactly the following order. This is not a script. So please cut and paste each of these commands one by one.
PS D:\> $syncdb.Unprovision()
PS D:\> $syncdb.Status=’Offline’
PS D:\> Get-SPServiceApplication
#Copy the GUID associated with the User Profile Service and paste it after “Id” in the next command:
PS D:\> $upa=Get-SPServiceApplication -Id $upa.ResetSynchronizationMachine()
PS D:\> $upa.ResetSynchronizationDatabase()
7) Provision the Sync DB:
PS D:\> $syncdb.Provision( )
8 ) Add the User Profile Synchronization service account (farm account) as the dbowner on the Sync DB (using SQL Server Management Studio).
9 ) Start the SharePoint 2010 Timer service
PS D:\> net start sptimerv4
10) Start the User Profile Synchronization Service in the Central Administration UI.
11) After the User Profile Synchronization Service is started, reset IIS.
PS D:\> iisreset
12) Create connections to data sources in the Central Administration UI.
13) Run full user profile synchronization.