@JLX89 What do you mean by " WordPress (Developer) Mulisite"?
You mean, you install an WordPress (Developer) instance and then manually implement what's required for running a Mulisite instance?
Now, no, installed themes being removed after you restart the WP Mutisite enabled app is not standard, nor even normal, so obviously something went wrong.
Were themes installed and activated before or after running in multisite mode?
Are all used themes from reliable developers' and original authors, or you versions borrowed activated from other sources?
Can you tell us more about what you did?
Yes, I've deployed a WordPress (Developer) fresh installation, used the CLI to enable Multisite, checked everything was working correctly initially. I've disabled the Redis Caching Plugin.
After converting to Multisite, testing, and activating the Redis Plugin, Purging Cache, and then again deactivating it for the time being. I've then moved on and installed a few themes such as Hello Elementor, Astra, and Divi -- Network Activated them and they are working initially. All themes, with the exception of the Divi theme are pulled from the WordPress repository directly -- Divi is a fresh download from Elegant Themes and manually uploaded.
After an undetermined period of time (inconsistent) all themes are removed with the exception of Twenty Twenty-Two. What seems to replicate this issue is when the app is restarted the themes seem to be removed.
@JLX89 Are you using a wp reset plugin?
The only thing I can see is that you have either a plugin or a 'bad coded' wp theme that is resetting your wp installation every time you start it.
Otherwise, I cannot see what would be causing this behavior. You are saying everything installed is 'legit', il's up to you to know. Now are all themes multisite compatible? Maybe, one is not and causing this glitch for some reasons.
In 99% of cases I've seen, and I've seen a lot, such behavior is due to some files within the wp structure, either from a plugin or a theme, which are not functioning as it should and most of the time it's because they've been modified for a hidden purpose.
Another, reason much less often seen, is a bug caused by some incompatibility between some plugins and some themes.
Generally speaking, wp mutisite works pretty well on Cloudron. I run one for years.
If you are certain all your files are from clean provenance, then try steps activation of themes and plugins. Like, activate a theme and restart wp and see what happens and so on.