UpdaterEngine fails to handle same node sibblings while renaming them from a UpdaterItemVisitor.QueryVisitor

In our project, we are currently working very hard to implement some updater modules that will upgrade our content from CMS 2.09.06 to 2.12.05.
We use the UpdaterItemVisitor.QueryVisitor to apply changes to nodes that match a given query.

Running the query that finds nodes on a given path of type hippo:handle, hippostd:directory, hippostd:folder with the repository tool, returns 440 results.
Our updatermodule that registers a UpdaterItemVisitor.QueryVisitor with the exact same query, eventually process 432 nodes successfully:

These are localized and renamed.

However,

Some nodes fail to process (exception are swallowed silently: see CMS7-3910 ) . It seems that a PathNotFoundException is thrown when processing nodes (hippo:handle) with same name siblings.
Our content contains nodes with the same name, such as:

hippo:handle /content/mynode
hippo:handle /content/mynode[2]

These are apparently not processed correctly when we rename them (using UpdaterContext#setName) from out of our updater.

Please help / look into this.

Kind regards,

Rob