Is the data delimited, then encoded or encoded, then delimited. In otherwords, do you need to do the decode before the split or the decode before the variable assignment?

If you need to the latter, shove a map {} in the middle.

($one, $two, ... $n) = map { decode_base64($_) } split m/\|/, $record;
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Note: I don't have the decode function in front of me, but I know others have provided a function for that.