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When you change over to battle.net account login information it appears that you can no longer sync accounts:
The instructions state:
1 Login to any character using AccountA.
2 Select "Sync account transfer file" from the Warehouse menu.
3 Logout. Go back to Account Screen, which saves the CarboniteTransfer.lua file.
4 Copy WTF\Account\<AccountA>\SavedVariables\CarboniteTransfer.lua to WTF\Account\<AccountB>\SavedVariables\CarboniteTransfer.lua
5 Login to any character using AccountB.
6 Select "Sync account transfer file" from the Warehouse menu. AccountB will now have Warehouse data from AccountA.
Instead of using seperate account names to differentiate the accounts, the lua and sync feature are using the single email address - which causes the data to be replaced instead of imported/exported.
A simple fix (until/if this will be fixed) is to go into the CarboniteTranfer.LUA of the first character file and do the following (assuming this is the first time syncing accounts)
1. Login to AccountA
2. Sync Account Transfer File (from within the Carbonite Warehouse)
3. Logout form AccountA
4. Copy CarboniteTransfer.LUA from AccountA to AccountB
5. Change ["<Battle.NET email address>"] to ["AccountName1"]
6. Log on to AccountB
7. Sync
8. Logout from AccountB
9. Copy CarboniteTransfer.LUA from AccountB to AccountA
10. Change ["AccountName1"] to ["Battle.NET email address"]
11. Change ["Battle.NET email address"] to ["AccountName2"]
Hope that helps anyone who is hitting this.