In the logs I do see that some files were changed from x2 to x1, but I don't see anything that points to any kind of error with those duplication tags.
As you know, duplication is defined by the tags on the pool parts (alternate data streams), and anything that changes / deletes those tags will alter the duplication on the pool. CoveFS does prevent duplication tags from being altered on the pool drive itself.
I've made a few enhancements to the duplication system that should make it more resilient to tag corruption:
* [Issue #28618] Always check duplication tags for consistency and perform repair before checking file duplication consistency.
* [Issue #28618] Duplication tags with a duplication count > 9 were not being repaired if damaged.
* [Issue #28618] Added additional log warnings when repairing duplication tags.
Also, if files need to be deduplicated (or duplicated), the duplication tags will now be re-read from the disk before any changes to the files are made. This is to make sure that the tags are not corrupted in memory.