When you link your devices, one of them being in Selective Sync or Synced mode, the folder arriving from another device will be automatically created in Default location defined in Sync preferences. If there is already a folder with the same name, Sync will add an index to a newly created folder.
To reconnect the folder and point it to the right location, right-click on the folder in Sync -> Disconnect. Then right-click again -> Connect and select the location (see below the page).
To avoid it you can choose how Sync will be treating newly added folders and pick an already existing folder target or choose another location for it.
All in all there are three synchronization modes: Disconnected, Selective Sync and Synced.
When Selective Sync or Synced modes are enabled, Sync will be putting all new folders into the default storage folder. However, if you want to set the location of a synced folder manually, you should switch the synchronization mode (on the device where custom location for new folders is to be chosen) into ‘Disconnected’:
Click 'My Devices':
Choose ‘This device’ > Select ‘Disconnected’:
Now if you add a folder on your other device, on this device it'll also be displayed in the Sync interface, however, no synchronization will start until you hit 'Connect'.
To connect the folder and pick custom location for it,
- hit 'Connect'
- In the next window show the path:
From now on, all new folders added on your other linked devices will be synced to this device in Disconnected mode. And every time you will be clicking 'Connect' you'll be able to choose a custom folder location.