as the d flag should cause unmatched items to be deleted?

No. The /d flag is specified as: "Delete found but unreplaced characters.". Ie. Any character unmatched by the searchlist is left untouched

Since your search and replace lists are equal length, any characters matched will always be replaced, so nothing will ever be deleted.

Deletions will only occur if the replacement list is shorter than the search list; including the frequently used case of a null replacement list.

In addition, if you also specify /c, then only the t (ie. pre-translated f) will remain:

$s = 'alter'; 

$s =~ tr[this][flip]cd; 
print $s;;
t
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So, to get the effect you expected you could do two passes:

$s = 'alter'; 

$s =~ tr[this][flip]cd; 
print $s; 
t

$s =~ tr[this][flip]; 
print $s;;
f
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From "Quote-and-Quote-like-Operators":
If the /d modifier is specified, any characters specified by SEARCHLIST not found in REPLACEMENTLIST are deleted.

This means if you do not specify a replacement for some character, it will get deleted, but only if it is matched.

  DB<112> $_="alter"
 => "alter"

  DB<113> tr/this//cd                 # delete anything except t,h,i,s
 => 4

  DB<114> $_
 => "t"

  DB<115> tr/this/flip/                # translate
 => 1

  DB<116> $_
 => "f"
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You could also do it with a single  s/// substitution, although it is messier and almost certainly slower than a double-tr/// approach:

>perl -wMstrict -le
"my %xlate = qw(t f  h l  i i  s p);
 ;;
 my $s = 'alters';
 $s =~ s{ . }{ $xlate{${^MATCH}} // '' }xmsgpe;
 print qq{'$s'};
"
'fp'
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Not sure if it's slower, 'tr///' doesn't allow variable interpolation.

Using it twice in a DRY way means putting the pattern into a variable which leads to eval :(

        Because the transliteration table is built at compile time, ne
+ither
           the SEARCHLIST nor the REPLACEMENTLIST are subjected to dou
+ble
           quote interpolation.  That means that if you want to use va
+riables,
           you must use an eval():
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Cheers Rolf

( addicted to the Perl Programming Language)