calculate md5 for each packet and output to new file with updated field

edit

Tested on WSL:

$ cat ./tshark_dupes
#!/bin/bash

tshark.exe -o frame.generate_md5_hash:TRUE \
-w MYDUPLICATES.PCAP -r MYFILE.PCAP \
  $(tshark.exe -o frame.generate_md5_hash:TRUE -r MYFILE.PCAP -Tfields -e frame.md5_hash \
  | sort \
  | uniq -c \
  | sort -n -r \
  | grep -v ' 1 ' \
  | tr -d '\r' \
  | awk 'BEGIN { printf "frame.number==0" } \
    { printf " || frame.md5_hash==%s",$2 } END { print "" }')

(This is more of a comment to go along with @grahamb answer but still haven't figured out how to add screenshots to comments)
MD5 hashes added in this commit
It is a generated field created if the preference frame.generate_md5_hash is set to TRUE.

epan/dissectors/packet-frame.c:
if (generate_md5_hash) {
<snip>
ti = proto_tree_add_string(fh_tree, hf_frame_md5_hash, tvb, 0, 0, digest_string);
proto_item_set_generated(ti);
}

doc/README.dissector:
proto_item_set_generated()
--------------------------
proto_item_set_generated is used to mark fields as not being read from the
captured data directly, but inferred from one or more values.

Simple example with with hashes copied to GUI display filter for testing:

$ tshark -o frame.generate_md5_hash:TRUE -r ./output.pcap -T fields -e frame.md5_hash | sort | uniq -c | sort -n | tail -5
      1 fd04a0e73be79cc94019a68a00666920
      1 feff0464f7b76af44a8d4acfc84bfafe
      3 42d98bc2aa77e47d09185cb8d98a0f9e
      3 a2e5d2e10a18a6bb30f6712088b7a293
      5 e29a39f345d4099d3205c9355a004bab
$

"the output file generated seems to be missing the MD5 hash"
That is correct. It is a "generated" field created from other data in the capture file.
It's ephemeral - only available if the preference is set to create it then gone at the end of the session.

If you plan to make use of it often then set the preference to TRUE and the hashes will be created and available for all files you open.

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