That certainly suggests something odd going on. After choosing the correct folder for it to scan, which excludes the other (outside of this) folders, you’re running the update process? You’ve also made sure the trash isn’t included in this folder? On my NAS, I had a case where it was including ‘to be deleted at some point’ trashed files, I had to be a tad more careful than I thought. The NAS was not deleting, just marking for eventual deletion at some future point.
If neither of these apply to you, I’d certainly recommend that you submit a system diagnostic within 10 minutes of experiencing this problem, and call Sonos Support to discuss it. Don’t post the resulting diagnostic number here, they get sensitive about GDPR.
There may be information included in the diagnostic that will help Sonos pinpoint the issue and help you find a solution.
When you speak directly to the Support staff, they have tools at their disposal that will allow them to give you advice specific to your network and Sonos system.