it does not say which node the file is supposed to be on.
I'm not familiar with this exact error message format, but assuming it means there's an Input/output error when reading /data/elasticsearch/security/nodes/0/indices/3dqdQFyJRyuUO_vVLon_WQ/2/index/_1bny.fdt then you're looking for a node holding a copy of shard 2 of the index with UUID 3dqdQFyJRyuUO_vVLon_WQ, so look for that UUID in GET /_cat/indices?h=uuid,index and then look for the node in GET /_cat/shards/$INDEX?s=s,p. If it's snapshot-related then it's probably the node with the primary shard.
Again assuming there's a problem reading _1bny.fdt, the error message Input/output error comes from the OS and normally means there's some problem with that node's storage. I'd suggest looking at its kernel logs with dmesg to confirm, and replace any faulty/suspect hardware before doing much more.
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