There is a config parameter to rescan you files on each request.
I used it once after i copied files into the datadirectory via cli an nextcloud did not recognize them.
You should only enable it temporary, since its is slow but it might help in your case if you do it once.
https://docs.nextcloud.com/server/latest/admin_manual/configuration_server/config_sample_php_parameters.html#filesystem-check-changes