I may be able to help you, but I need to make a few assumptions and/or ask some questions. Are you using SQL Server or Oracle? It sounds like you're interested in creating a two-way replica but I cannot be sure. I am going to use Oracle as my basis for some of the answers for the time being.
First, let's make sure that the previous replica version is removed from the geodatabases before trying to create a new one. Keep in mind that whenever your unregister a replica (i.e., delete its version) from a geodatabase, it should be done while connected as the replica owner and not necessarily the SDE user. Open ArcCatalog and connect to both of your geodatabases as the replica owner, then right-click them and expand the Distributed Geodatabase menu, and look at the Manage Replicas item. It should be grayed out... if not, then click it to see the list of replicas. Right click each one in the list and choose Unregister.
Next, go ahead and issue the following query to your TWO geodatabases using a tool like Oracle SQL Developer (otherwise known as the parent and child geodatabases especially if you're using a 1-way):
SELECT * FROM SDE.VERSIONS
WHERE NAME LIKE '%SYNC_SEND%'
If any versions are returned, you'll need to delete them using ArcSDE command line as shown below. Substitute the SYNC_SEND version name with one from the result set above. Replica versions are hidden and can't be seen in ArcCatalog... only directly from the GDB using SQL. Replica versions always begin with SYNC_SEND.
sdeversion -o delete -V SYNC_SEND_X_X -u <replica_owner> -p password -i esri_sde -s DBSERVER -D db_name
This should get you to the point of starting over with a clean slate. You'll need to re-create / register the replica again. To do this, make sure the connection you use for ArcSDE contains the intended replica owner account as well as the intended transactional version.
Once the replica is created and registered in both geodatabases, make some edits to the parent version of the replica and then try to sync the changes via ArcMap. This can actually be done with the "connected" tools or the disconnected tools. Check the ReplicaLog.dat file at the following location (assumes Windows 2008 R2): C:\users\<your_domain_user_account>\AppData\Local\Temp. Open the file with a text editor and see if there are any errors throughout. If not, go back to ArcCatalog's "Manage Replica" GUI from the Distributed Geodatabase menu, right click your replica in the list, and choose View Log. If your results say "ERROR" then right click the line item in the list and view the error report.
Let me know the results and we can try to troubleshoot this together further.
