No. The only way chomp would remove two characters is if $/ was two characters long, and $/ is \n by default in Windows.

>ver

Microsoft Windows XP [Version 5.1.2600]

>perl -le"print length $/"
1

>perl -le"$,=' '; print map { uc unpack 'H*', $_ } $/=~/./sg"
0A
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The reason this isn't a problem is that the PerlIO layer :crlf is used by default in Windows, and that layer converts CRLF to LF on read and LF to CRLF on write.

>>foo echo foo

>debug foo
-rcx
CX 0005
:
-d100 l5
0B0B:0100  66 6F 6F 0D 0A                                    foo..
-q

>perl -le"print length <>" foo
4

>perl -le"$,=' '; print map { uc unpack 'H*', $_ } <>=~/./sg" foo
66 6F 6F 0A
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Builds of Perl without PerlIO (i.e. before 5.8) use the underlying C library, and it does the same thing.