We had a problem with our owncloud instance 9.0.2. We reach our server size quota and some files couldnt be uploaded to server. The server just created the folders but appear like files, i cant open or remove them (not option to remove on this files). If i click i get an error message "service unavaliable Request ID: ............"
please first update to the latest stable version of oC 9.0.x which is 9.0.4. Afterwards you can try to rescan your filesystem by using the occ files:scan command documented here:
I followed the steps you metioned and the problem is solved. I only scanned the directory with the problem with --path param. 5 minutes later the was solved.