Certificate file directory /config/filestore/files_d/Common_d/certificate_d

I have a pair if HA devices running 12.x, and I also have an external certificate management program. What was identified by the external cert program is that the file store in /config/filestore/files_d/Common_d/certificate_d is not in sync across HA devices.

In the GUI or TMSH they are in sync but not the actual file directory. How can I go about and get these directory's in sync, or how can I manually remove the non TMSH referenced certificates without potentially causing any config load issues?

Thx