I can confirm after performing a backup the node is not in base but still referenced by its parent.
From the description it sounds like something caused data corruption w/ regards to child references. I suggest you migrate to ModeShape 5 which doesn't use Infinispan and which should hopefully be more robust data-integrity wise.
There is not automated way to fix data corruption. If applicable, you could try explicitly removing and recreating the parent and the child nodes. Also, if you're restoring from a corrupted backup, you can manually edit the backup (the content of the backup is plain text JSON) and remove from the parent the corrupt child reference.