Because of the "pop @F" in your code. See the text in red below.

Code:

perl -i.bak -aF/\\t/ -lne 'BEGIN{%m=map {chomp;(split/[\s\.]/)[1,0]} <STDIN>};($r)=grep {$x=$_;grep {$x=~/$_/} keys %m} (split/\;/,$F[$F[6]=~/exonic/?11:8]);$r=~s/.*?(NM_.*)$/$1/;pop @F;print join("\t",@F,$r)' file2.txt < file1.txt

Here's the documentation of the "pop" function: pop - perldoc.perl.org


Skipping the header will retain the "Sanger" column header.
And the "pop" will then remove the last column from the remaining rows.

For the same reason the "Sanger" column header gets removed - the "pop" function.

I did not understand this statement.
The last field in line 1 of "file2.txt" is "Sanger". It is not empty.