This is expected behaviour, the user which is configured during resource configuration will fetch table and schema having access. Every time you run the resource in EDC it delete and repull all the metadata, If the user access is removed from that schema and table it will be lost on next run.
as a minor correction - the scanners will not delete all objects and then rescan. The scanners will delete any objects that are no longer existing.
for the case where you don't have access to a table, the scanner will think that the table has been deleted.
the staging process will be used to determine if any changes are needed (add/update/delete)