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But what is the logic? We could remove #1 and #3, or #1 and #4, etc. What's the rule?

And use those code tags... ;)

Yes, you made the right choice to try sed:
$ sed "s/|$//" file
aaa|bbbb|cccc|dddd|fff|dsaaFFDFD
Adsads|sas|sa|as|asa|saddas|dsasd|sdad
dsas|dss|sss|sss|ddd|dssd|rrr|fddf...