Since the migration process seems to delete the contents of the autoupgrade/download folder 
True. Forgot to remove this when picking this feature from module tbupdater. 
Here's the patch (just find and delete these four lines):
```diff
             // regex optimization
             pregmatch('#([0-9]+.[0-9]+)(?:.[0-9]+){1,2}#', _PSVERSION_, $matches); 
         $this->nextQuickInfo[] = sprintf($this->l('Downloading from %s and %s'), $this->upgrader->coreLink, $this->upgrader->extraLink);
         $this->nextQuickInfo[] = sprintf($this->l('Files will be saved to %s and %s'), $this->getCoreFilePath(), $this->getExtraFilePath());
-            if (fileexists($this->tools->downloadPath)) {
-                Tools::deleteDirectory($this->tools->downloadPath, false);
-                $this->nextQuickInfo[] = $this->l('Download directory has been cleared');
-            }
+
             $report = '';
             $relativeDownloadPath = strreplace(PSROOTDIR, '', $this->tools->downloadPath);
             if (ConfigurationTest::test_dir($relativeDownloadPath, false, $report)) {
                 $timestamp = time();
                 $res = $this->upgrader->downloadLast($this->tools->downloadPath);
``` 
This will also go into the next release, of course.