To preface, I’m a Boxcryptor consumer and not a developer so there may be a better option.
Through trial and error, something that may help you regarding the unencrypted recent files is to “lock” the files in the Boxcryptor app.
Once you enable the feature “File Protection” under settings tab, “Lock” becomes an option under the home tab.
This has allowed my recent files to be inaccessible for viewing or selecting.
One thing I’ve noticed is that I will constantly receive a notification to unlock Boxcryptor in order to view access files even if I’m not trying to actively access files within the Boxcryptor section of the FilesApp. I’ve turned off notifications to work around this issue.
Regarding deleting, the files in your recent tab are direct links to the files synced to the cloud of choice. If you delete them in recent, you’re deleting them from the cloud. I don’t know that there is an option to turn of recent files in the FilesApp. I’m almost certain that is an iOS feature that can’t be turned off and may require a feature request through Apple.
I hope this helps you.