Long story short. I made a bunch of subdomains to sort all my storage into subdomains. Files into download.domain.com. Images into images.domain.com etc.
So far so good.
Apparently the permissions that is set when creating a subdomain do not work properly when then changing the storage in ACP. So not everything was moved but ACP still deleted the content left over on the original storage. After a lot of back and forth I decided to restore from a backup, but dumb as I am I didn't make a full backup before I started the storage move, since I didn't know permissions would cause so many issues. So, I restored all the files which I had a backup of, but the database backup was 1 month old.
Now, IPS is working correctly so far but I cannot save storage settings. I'm getting...
RuntimeException: (0)
#0 /home/client/domain/applications/core/modules/admin/overview/files.php(418): IPS\_File::getClass()
#1 /home/client/domain/system/Dispatcher/Controller.php(107): IPS\core\modules\admin\overview\_files->settings()
#2 /home/client/domain/system/Dispatcher/Dispatcher.php(153): IPS\Dispatcher\_Controller->execute()
#3 /home/client/domain/admin/index.php(13): IPS\_Dispatcher->run()
#4 {main}
Backtrace
#0 /home/client/domain/init.php(1038): IPS\_Log::log()
#1 [internal function]: IPS\IPS::exceptionHandler()
#2 {main}
...When saving storage setting after selecting a new location. All permissions are set and in order.
There is no errors in the ACP support section.