Please help. Lost lots of files this way since I thought everything was being uploaded. Nothing is - only with iOS it’s working.
Cryptomator for Windows does not sync anything. This is the job of your cloud providers sync app. Please check if you have configured it according to your vault location and check if the sync is up and running.
I use it for years and never had any issues on mobile. Only on desktop. Any tips besides “check your sync”. I bought Cryptomator 1 and 2. Support will be nice. And not the regular BS please.
How about you keep a calm head and be nice. 
As @Michael already mentioned, Cryptomator does not sync anything on Desktop, it just creates/deletes/modifies files at the vault storage location. The there can be two points of failure on the Cryptomator side:
- Files were not created, event though they should have.
- The iOS-App ignores the created files.
The first one you can easily test: Go to the storage location of your vault and search for files which has a very recent lastModified date. Then see, if this change is also present in the cloud with the same file.
Additionally you can run the health check and see if there are any warnings, that a directory is “orphaned”.
The latter one is harder. If possible, you can download the vault on another device/user account and open it there with Cryptomator. If the most recent changes are present, then the error is on the iOS side.