Have you checked here:
If your files are available on your iCloud Drive app/icon on iCloud.com?
If not there, click at top right corner on your name > iCloud Settings > scroll down to the bottom of the page > look for Advanced and restore files / Dateien wiederherstellen / recover files > click on it and pick the files to recover.
If your files are not available there, than I suggest, even it might be a pain if you have multiple files, you move/copy them to your iCloud Drive. So you save them from being synched and deleted. I would be afraid of that too. This can be done in offline mode. (just tested it)
Here is how you can move them:
- Open Numbers on your iPhone (I believe the files are there, correct?)
- Tap in the lower left corner.
- Tap on 'Bewegen' / 'Move'
- Tap on the file to move
- Scroll down and tap on iCloud Drive (this will move the file to iCloud Drive) even if its shown within the App without the cloud icon! (because you have a local copy)
instead of activity 3 move you can also copy to iCloud Drive, Dropbox, your Mac (if you have one), etc.
before you copy/move in activity 5 you may want to create a new folder in your iCloud Drive like 'Numbers Backup' so its not stored on the highes hirachy on your iCloud Drive.