Problem solved! 

I have solved upgrading problem due to hash failing by disabling "check_module_hash"

in a file: /studio/classes/BxDolStudioUpdater.php

here around line 31 by commenting out with double slash "//" :

//     'check_module_hash' => array(
//      'title' => _t('_adm_txt_modules_check_module_hash'),
//       ),

and I just temporary removed the code for  "check_module_hash " :

        //--- Check hash ---//

removed code:

        $aFiles = array();
        $this->hashFiles(BX_DIRECTORY_PATH_ROOT . 'modules/' . $this->_aConfig['module_dir'], $aFiles);
        list($aFilesChanged, $fChangedPercent) = $this->hashCheck($aFiles, $aModuleInfo['id']);
        $bAutoupdateForceModifiedFiles = getParam('sys_autoupdate_force_modified_files') == 'on';
        if(!empty($aFilesChanged) && !$bAutoupdateForceModifiedFiles) 
            return array_merge($aResult, array(
                'code' => BX_DOL_STUDIO_IU_RCE_MODIFIED,
                'message' => $this->_displayResult('check_module_hash', false, '_adm_err_modules_module_was_modified', $bHtmlResponce),
                'result' => false
            ));
        else if($fChangedPercent > BX_FORCE_AUTOUPDATE_MAX_CHANGED_FILES_PERCENT && $bAutoupdateForceModifiedFiles) 
            return array_merge($aResult, array(
                'code' => BX_DOL_STUDIO_IU_RCE_CHECKSUM_FAILED,
                'message' => $this->_displayResult('check_module_hash', false, _t('_sys_upgrade_files_checksum_failed_too_many_module', round($fChangedPercent * 100), $aModuleInfo['title']), $bHtmlResponce),
                'result' => false
            ));

After that upgrade of failing modules upgrade for Persons and Protean succeeded. 

In Studio -> Apps Market I can now see:

Persons
BoonEx • 11.0.1

and

Protean
Boonex • 11.0.3

as expected.

I did that because I was 100% sure that I haven't change any modules files so it was  strange why "Check hash " didn't pass.
I restored studio/classes/BxDolStudioUpdater.php after upgrade.