The first question would be: "Does the CSV have a header line, or can it be made to have a header line?". If so, your initialisation could be much simpler. And the ~ does not have to be escaped at all.

$ cat data/objectives-cqdc.txt
Obj~PosNbr~Year~Div~AVP~Dept~SDescr~Major~Methods~Results~Accompl~JanU
+p~LDescr~Changes~Chars~Goals~Budget~CFObj
20140000020~00001576~2014~"testdata"~"testdata"~"testdata"~-~0~-~"Inse
+rted on December 10, 2013"~-~-~-~-~20000000001~20130000001~1~-
$ cat test.pl
use 5.16.2;
use warnings;

use DBI;
use Data::Peek;

my ($Cposition, $Cyear) = ("00001576", 2014);

my $dbh = DBI->connect ("dbi:CSV:", undef, undef, {
    f_dir        => "data",
    f_ext        => ".txt/r",
    csv_sep_char => "~",
    });
my $sth = $dbh->prepare (qq{select * from "objectives-cqdc" where PosN
+br = ? and year = ?});
$sth->execute ($Cposition, $Cyear);
while (my $row = $sth->fetchrow_hashref) {
    DDumper $row;
    }
$ perl test.pl
{   accompl          => '-',
    avp              => 'testdata',
    budget           => 1,
    cfobj            => '- ',
    changes          => '-',
    chars            => '20000000001',
    dept             => 'testdata',
    div              => 'testdata',
    goals            => '20130000001',
    janup            => '-',
    ldescr           => '-',
    major            => 0,
    methods          => '-',
    obj              => '20140000020',
    posnbr           => '00001576',
    results          => 'Inserted on December 10, 2013',
    sdescr           => '-',
    year             => 2014
    }
$
[download]

Also note that file has been deprecated in favor of f_file to be more consistent with DBD::File specifications. An aditional disadvantage of using specific csv_tables initialisation is that the table name in not case insensitive anymore and that the initialisation takes MUCH longer, as DBD::CSV will scan the default f_dir (defaults to ".") for usable table names possible taking a lot of IO you do not want. Your new code when not having a header could look like this:

use DBI;
use Data::Peek;

my ($Cposition, $Cyear) = ("00001576", 2014);

my $dbh = DBI->connect ("dbi:CSV:", undef, undef, {
    csv_sep_char => "~",
    csv_tables   => {
        JPDObj   => {
            f_file    => "data/objectives-cqdc.txt",
            col_names => [qw(
                Obj PosNbr Year Div AVP Dept SDescr Major Methods Resu
+lts
                Accompl JanUp LDescr Changes Chars Goals Budget CFObj 
+)],
            },
        }
    });
my $sth = $dbh->prepare (qq{select * from JPDObj where PosNbr = ? and 
+year = ?});
$sth->execute ($Cposition, $Cyear);
while (my $row = $sth->fetchrow_hashref) {
    DDumper $row;
    }
[download]