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.

Maybe not using MainLoop at all works? See tk close window and the replies, which suggest that using $dialog->Show() works for showing a dialog.

But, I am able to destroy the window, but the control is not coming back to the calling function.

---

All is well. I learn by answering your questions...

Maybe you are properly leaving the MainLoop, but Tk does not want to restart it? I don't know. I think the better approach is to not start the MainLoop at all.