@niko You have to convert the app into a Cloudron app for all this to reliably work. We don't support running/installing other things other than Cloudron on the same server. This is because Cloudron will overwrite nginx configuration etc from time to time (for example, updates bring in new configuration).
If your app has a Dockerfile, you can make it a custom app with not too much work - https://docs.cloudron.io/custom-apps/tutorial/ . Custom app will automatically get certs, backups, restore, clone features etc with no extra work. What framework/language does your app use?