Hey,
I was wondering if the Cryptomator files are stored in the iCloud or somewhere in my phone. I have this question because I noticed that I can access all my files while being in flight mode - even when I cleared the cache. Clearing the cache removes the file size from my storage but accessing them again shouldn’t be possible then when being offline or am I wrong? Where do the files go?
I hope somebody can help me out. 
iCloud Drive is a special case on iOS. Cryptomator accesses iCloud Drive via the “local file system”. You may have noticed that your iCloud Drive files (that are not encrypted) are also available when you’re offline. That’s what Cryptomator is basically just trying to do. If it’s locally available, it will decrypt the local file directly. If it’s not locally available and you’re offline, the access will fail because it’d have to download the encrypted file first.
I see, but clearing the cache removes the files from storage so how is it possible that u can redownload this files while being in flightmode? Does the storage actually gets cleared up or is that a lie from Apple? (Edit: iCloud Drive only shows me 560mb storage usage but my Cryptomator files are around 6gb, so why can I still access all of my files while being offline?)
Just to be clear by deleting the cache you mean the operation inside the Cryptomator iOS app right? Does it show you Zero KB after you‘ve cleared the cache?
In any case Apple could and probably have actually implemented their own caching strategy for iCloud Drive on iOS and we have no control over this cache.
If you want you could verify the space used by the Files app (in the iOS settings) has been reduced by the size previously displayed in the Cryptomator app settings after you have cleared the cache via the Cryptomator iOS app.