If you’re in a position to do some testing, try out our Periscope module:
It adds both Embedded View + and Flex Repeater + components, that do all their parameter mapping on the gateway side, preemptively start their views, and expose a key property to allow for correct instance insertion/deletion.
It’s not going to be a silver bullet for any misconfiguration that you might currently have, but in our experience it solves a lot of the current weirdness with deeply nested embedded views.