Set a flag when the condition occurs and check for it.

our $SKIP_REST_OF_FILE;
sub trap_substr_warning {
    my $e = $@;
    if ( $e =~ /whatever/ ) {
        $SKIP_REST_OF_WARNING = 1;
    }
    else {
        print STDERR $e;
    }
}
sub find_process {
    local $SKIP_REST_OF_FILE = 0;
    local $SIG{__WARN__} = \ &trap_substr_warning;
    ...
    if ( $SKIP_REST_OF_FILE ) {
        ...
    }
}
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