Updating Aqua Theme from old version to latest version causes settings loss

Upon upgrading old Aqua theme to new theme, i get this pop up in control panel:

OptionTree has outdated data that should be removed. Please go to OptionTree Cleanup for more information.

And there after, all Posts/Pages settings like sidebars setting disappears. Problem is, i have 600 + pages and different settings for each to the sidebars.

The footer widgets had been reset as well. ( this is OK. I only need to edit 4-5 widgets manually back)

Any workaround so that the settings don’t get lost?