You can adapt the steps from Migrating from User to Service install on Windows, version 3, to move the working folder of duplicati to a dir that does not get re-written on windows update. Eg, C:\ProgramData\Duplicati\Data. If it’s worth it to you.
Yeah, we’ve been getting pretty consistent result. locked/temp/rapidly changing files are the culprit. It would be nice to confirm your situation is the same. Instructions here.