Awkward Magento 2.1.3 to 2.1.13 upgrade error

[jalnet]

Hello,

I've tried to update my store from 2.1.3 to 2.1.13. I did it on deployment server with success following those steps:

composer require magento/product-community-edition 2.1.13 --no-update

composer update

rm -rf var/*

php bin/magento setup:upgrade

php bin/magento cache:flush

php bin/magento setup:static-content:deploy

php bin/magento setup:di:compile

php bin/magento indexer:reindex

chown -R apache:apache /var/www/html/

php bin/magento cache:flush

When I did exactly the same thing on production,  after the last step ( flushing cache ) almost all my files from magento root folder were deleted. 

I've restored my server from last snapshot right away, so I don't have any logs.

I did it twice, same thing happened every time.

Any idea what this could be?

[Manthan Dave]

Hi @jalnet

there should be a two reasons , on your production setup , check which magento environment it is in there ? - is it in production ?

If yes kindly change it into developer mode by running this command - php bin/magento deploy:mode:show developer and then try to upgrade.

second and most important thing is ownership and permission , its depends which user are you using to upgrade the version ? if should be with magento user.

so refer this link for permission and ownership issue - https://devdocs.magento.com/guides/v2.1/comp-mgr/cli/cli-rc1-samp.html

[Mukesh Tiwari]

Hi @jalnet

Not sure , but you make check composer update deleted all files in mage2 folder once.

[jalnet]

I've tried that, it's not working, because composer is deleted as well.

[jalnet]

I tried a different approach. I moved my website to a new folder, I upgrade it to last version 2.1.15, I test it, everything was fine. So I've decided to move this to root folder.  It worked for a few seconds, and then was gone, all files deleted again. 

[jalnet]

If I stop cron jobs everything works fine. However, when I'm starting cron jobs back everything gets deleted.

Any idea what can cause this?