Hierarchy creation question after upgrading to 3.5

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I upgraded our cloudserver to 3.5.6 and updated 2 of the 4 connected ES devices to 3.5.6 as well leaving 2 ES devices connected as 2.8.8. On the 3.5.6 ES I enabled the persistent TCP to update the hierarchy on the target to match the source. I noticed that the target now has an NEW directory MU2 and the structure is switched around so SITES are under MU2 directory even though on the ES MU2 is under SITES. Why is this happening? The tree structure on 2 other 2.8.8 ES connected devices work fine. I want the ES to have the same structure as the cloud and not create a new MU2 named directory off the cloud's root?

This is the ES hierarcy...

[ two folders and one nest of folders 4 deep ]

This is the cLoudserver's hierarchy ... I have created the structure I want but the ES creates a new MU2 directory above and does not use the existing structure.

[ the two folders, the four deep folder with some extras, 
and then the MU2 directory with the four deep folder 
possibly inside it, but only revealed two levels deep ]

Hi Phillip,

In the image, it appears as though the directories from the ES have been created on the cloud instance, which is all the sync can do. Are you saying that if you delete the errant MU2 folder and those beneath it, it comes back? Might you have configured a hierarchy prefix on the data source or publisher?

Ah I did use a xid prefix and this must have put a prefix path in the target that see now on the cloud data source. can I safely delete this path prefix . Do I need to stop the datasource to delete this? Will I lose any data if I delete the prefix??

Whenever a publisher or data source is saved, it is stopped and then started. You must save your changes for them to be in effect.