Theme settings vanish on Update to 2.1

Hello

I follow the following process to update my theme:

1. Upload arcane.zip to /wp-content/themes
2. Rename arcane folder to bak.arcane
3. Login to SSH and unzip arcance.zip
4. grant chown to web user to directory /wp-content/themes/arcane
5. Login and check website
6. If all ok delete bak.arcane
7. Upload any plugin updates.

I have followed this method for all updates and its worked except when now updating from 1.8.1 to 2.1. When I attempted to update this time, i lose my entire theme settings and the theme seems to lose its ability to read the previous ones as it displays the default arcane colour and logos. There is no option under appearance for theme settings. There are no errors being written to the error_logs

I will reply with private reply with FTP details and Admin login for website. If FTP fails to connect let me know it may be geoip blocking.

IMPORTANT NOTICE TO SUPPORT(@ZORS):
VS Composer is premium, please do not delete this or any other premium plugin such as UberMenu. Please act with care when when accessing FTP.

The new theme is under new.arcane as I cannot risk leaving the broken branding(Reputational damage and what not)