There are a number of discussions where this is explained, in short:
Confirmed downlinks depend on all uplinks to get through. If the uplink with the ack is missed there will be another downlink with whatever data was sent before. Now your embedded device needs to deduplicate those downlinks or process the same information twice.
Then there is the issue you encountered where the downlink causes the device to reset (the stack or all of it doesn’t matter) so no ack will ever be arriving. You are stuck in a loop…
The best way to handle downlink acknowledgment is at application level. When a downlink is received and handled update a field that will be in all your uplinks so even if a couple of uplinks are missed your application still knows the device got its instructions and processed them.