I used to handle 250 employees. The filing system will depend on what you want to achieve. We used to file based on employee ID with further subdivision based on documents within a folder, i.e., CV, Education Certificate, Contract, Increment, disciplinary action, etc. This folder was also used to upload files on the HRM server. Yes, we were duplicating the work, but that was inevitable. Not sure why you want to metafile to search stored files when you can search for details within HRMS. I would appreciate knowing what exactly you are trying to achieve and the challenges you want to resolve. Additionally, which HRMS software do you use?
Regards,
Ukmitra