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I had a similar problem and TAC told me it was because I used the http file transfer via the gui instead of using SCP. They instructed me to only copy the image to the APIC using SCP. FWREPO showed it did not copy to the other 2 APICs.
Would this squelch a Leaf to Spine port if that disconnected? That would be bad if you did not get the alert for a link like that dropping. What if a APIC dropped a link to a Leaf, would that be squelched as well?