We've seen sporadic reports of files disappearing after updating PDF Viewer. The process of updating an app is managed by Apple directly, and isn't something we can customize or debug. PDF Viewer does not modify any files stored by the user after an update.
PDF Viewer uses the standard iOS document browser from Apple’s Files app. Apple’s secure and private design means PDF Viewer is only able to read and modify files that you choose to open, which means it has no capability to delete all your files.
If files appear missing, this is most likely an issue with a cloud storage provider or with the iOS document browser. In many cases, such issues are resolved by restarting your device. The missing files usually appear again in the appropriate location after a restart.
Apple both controls iCloud Drive, the local storage of the document browser and the upgrade process. We already notified Apple that we see rare reports of issues in that process, and it helps if you also reach out to them via https://support.apple.com/
If files have been deleted from iCloud Drive, check Apple's Recover deleted files on iCloud guide.