You have not specified the routing protoco that you are running, but I am going to guess that it is EIGRP. I have experienced similar symptoms in a network running EIGRP. When we have experienced these symptoms there was some evidence that we were experiencing one way traffic (EIGRP hello was transmitted from one peer to the other but not transmitted in the other direction). This produced symptoms of neighbor down (retry exceeded) then neighbor up.
Can you tell us a bit about the topology in which you are experiencing this? And can you check for the possibility of one way traffic?
HTH
Rick
HTH
Rick
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