Since it seems that you are using Synology NAS, I have a few tips for you. I use Syncthing and Resilio on all of my Synology’s for different tasks.
First, check whether you have activated the “Ignore” permissions for each peer (Edit> Advanced> Permissions). Experience has shown that this eliminates most of the inconsistencies.
If this is already activated, deactivate it once, let the scan run completely and activate it again. This change also often helps. I don’t know why.
Doesn’t help either, the following. Provided that you have correctly set the user rights for the Syncthing User, you should try to delete the Synology ACLs to the subfolders of the peers. I always do this with WinSCP by setting group and owner to “root” and granting full rights, octal 0777. This deletes the Synology ACL’s to the subfolders. You can set this again by transferring the rights to the subfolders in the corresponding folders in the Synology DSM file manager.
Due to inconsistent databases, I also manually deleted and re-indexed all of my databases a few days ago, which actually seems to be the best way to get a clean system. Since then everything has been going very well and wherever peers overlap between syncthing and resilio, the same numbers are displayed for the elements everywhere.
Finally, how did you install Syncthing on your NAS?