if you start Azure Data sync between two databases in two way mode and you have data to be merged in both (or more) databases you might found that also with relatively small amount of data the initial sync is very slow and might cause blocking issue with your application.
more information about it can be found here: Avoid slow and costly initial sync
start the sync when you have data in only one database on the sync group.
in case you have data to sync in both locations and data need to be merged you should do that manually.
note that even if you have identical data among members in the sync group, Data Sync consider this as data that need to be merged as there is no way for Data sync to confirm this is identical unless it goes row by row which we described in symptoms. therefore our recommended approach is to run initial sync with data in only one database.
I found that it will be very easy to use the Data compare option provided by SQL Server Data Tools
if you are not familiar with that please read the below articles:
I hope you found that information useful, please do share your comment about your experience.