You may have to delete the existing project (don't try this next time) (Assuming Pootle in /var/www/pootle)
cd /var/www/pootle
source env/bin/activate
pootle fs fetch --force MYPROJECT
pootle fs sync MYPROJECT
If you need to delete your project (assuming it is called MYPROJECT)
cd /var/www/pootle/tmp
chown -R www-data:www-data MYPROJECT
Then you can delete it through the user interface.