If $. is 0 (first line of the file), skip to the next iteration. … On all subsequent iterations $. will no longer be zero…
The number of the first line of the input file is 1, not 0. So you need to use an explicit comparison operation.
perl -pli.bak -e 'substr($_, 18, 1) =~ tr/Y/H/ if $. > 1' filename
Here's the same thing using a regular expression.
perl -pli.bak -e 's/^.{18}\KY/H/ if $. > 1' filename
Jim
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