I've refactored your code to use strictures and get rid of various global variables. The window variable and file path get passed into the OK dialog as closures instead of using global variables. The code now works as I understand you would like.

use strict;
use warnings;
use Tk;

my @files = 1 .. 10;

for my $file (@files){
    {
     my $mw = MainWindow->new;
     $mw->geometry("400x120");
     $mw->title("CI Generation");

     #-----------------Frames-----------------------#
     my $main_frame = $mw->Frame()->pack( -side => 'top', - fill => 'x
+' );
     my $top_frame =
        $mw->Frame( -background => 'light green' )->pack( -side => 'to
+p', -fill => 'x' );
     my $left_frame =
        $mw->Frame( -background => 'white' )->pack( -side => 'top', -f
+ill => 'x' );

     $top_frame->Label(
        -text => "Copy generated *.[ch] files to host repository",
      )->pack( -side => 'top' );

     $left_frame->Label(
        -text       => "Enter host repository path:",
        -background => 'yellow'
       )->pack( -side => 'top', -fill => 'x' );

     my $pathEntry = "path/$file";

     my $entry = $left_frame->Entry(
           -textvariable => \$pathEntry,
            -width => 50)->pack( -side => 'top', -fill => 'x' );

     my $buttons =
        $left_frame->Frame()->pack(-side => 'bottom', -fill=>'both', -
+expand=> 0);

     my $executeButton=
        $buttons->Button(
                  -text => "Continue",
                  -command => sub{okbutton($mw, $pathEntry)},
                  -width => 20,
                  -height => 2,
                  -underline => 11
                  )->pack(-side => "left");

     my $exitButton =
        $buttons->Button(
                  -text    => "Cancel",
                  -command => sub { exit 1; },
                  -width => 20,
                  -height => 2,
                  -underline => 11
                 )->pack(-side => "right");
    MainLoop;
    }
}


sub okbutton{
    my ($mw, $pathEntry) = @_;
    print $pathEntry;

    if (!$pathEntry) {
        $mw->messageBox(
            -icon=>'error',
            -title=>'Error on Repository Path',
            -message=>"Error: Repository path should not be empty."
        );
        return "";
    }

    if ($pathEntry !~ /[1245679]/) {
        $mw->messageBox(
            -icon=>'error',
            -title=>'Error on Repository Path',
            -message=>"Error: Repository path can not include 3, 8 or 
+0."
        );
        return "";
    }

    $mw->destroy if Tk::Exists($mw);
}
[download]

Note that I've altered the OK dialog file tests a little to make the code testable without needing a file system.