It might be also possible that these files are now gone due to the mentioned bugs. There are only few users / developers with knowledge about the old encryption left so you're mostly on your own with such issues.
Depending on the size of your installation / user base the cleanest way is probably to do a fresh installation of 9.1.4 and let your users re-upload their files.
Then you should also reconsider the usage of the encryption app. The following documentation at  provides some notes about the use case of the encryption app. If you don't use external storages the encryption app brings just another layer of complexity without any security benefit:
Encryption keys are stored only on the ownCloud server, eliminating exposure of your data to third-party storage providers. The encryption application does not protect your data if your ownCloud server is compromised, and it does not prevent ownCloud administrators from reading users’ files. This would require client-side encryption, which this application does not provide. If your ownCloud server is not connected to any external storage services, it is better to use other encryption tools, such as file-level or whole-disk encryption.