drush deleting sites folder

I ran my drush update script this morning and it deleted my sites folder. Luckily I had a back up of one site, the other site I wasn't so luck with.

I have updated drush head to latest to double check and run the update again with the same result. Output below;

Refreshing update status information ...
Done.
Update information last refreshed: Mon, 09/11/2009 - 14:04

Update status information on all installed and enabled Drupal modules:
Name Installed Proposed version Status
version
Administration menu 6.x-3.0-alpha3 6.x-3.0-alpha3 Up to date
Advanced help 6.x-1.2 6.x-1.2 Up to date
Backup and Migrate 6.x-1.2 6.x-1.2 Up to date
Drupal 6.14 6.14 Up to date
Charts 6.x-1.0-alpha6 6.x-1.0-alpha6 Up to date
Charts And Graphs 6.x-1.0-alpha4 6.x-1.0-alpha4 Up to date
Content Construction Kit 6.x-2.5 6.x-2.6 Update available
(CCK)
Date 6.x-2.4 6.x-2.4 Up to date
Mailhandler 6.x-1.8 6.x-1.8 Up to date
Network Manager 6.x-1.2 6.x-1.4 Update available
Node import 6.x-1.0-rc4 6.x-1.0-rc4 Up to date
Support Ticketing System 6.x-1.2 6.x-1.2 Up to date
Support Timer 6.x-1.0-beta1 6.x-1.0-beta1 Up to date
SWFObject API 6.x-1.0-beta1 6.x-1.0-beta1 Up to date
Token 6.x-1.12 6.x-1.12 Up to date
Views 6.x-2.7 6.x-2.7 Up to date
Views Bonus Pack 6.x-1.0-beta4 6.x-1.0-beta4 Up to date
Views Charts 6.x-1.0-alpha1 6.x-1.0-alpha1 Up to date
Views Group By 6.x-1.0-rc2 6.x-1.0-rc2 Up to date
Zen 6.x-1.0 6.x-1.0 Up to date

Code updates will be made to the following projects:
Content Construction Kit (CCK) [cck-6.x-2.6], Network Manager [network_manager-6.x-1.4]

Note: Updated modules can potentially break your site. It's not recommended to update production sites without prior testing.
Note: A backup of your package will be stored to backups directory if it is not managed by a supported version control system.
Note: If you have made any modifications to any file that belongs to one of these projects, you will have to migrate those modifications after updating.
Do you really want to continue? (y/n): y
Project cck was updated successfully. Installed version is now 6.x-2.6.
Project network_manager was updated successfully. Installed version is now 6.x-1.4.
Backups were saved into the directory [ok]
/var/www/helpdesk/backup/modules/20091109140444.

Fatal error: require_once(): Failed opening required './sites/all/modules/views/includes/view.inc' (include_path='.:/usr/share/php:/usr/share/pear') in /var/www/helpdesk/sites/all/modules/views/views.module on line 511
Drush command could not be completed.