Following up from this issue I noticed I have the following errors in the VPXD logs...
[04052 info 'Default'] Registry Item DB 5 value is '50'
[04052 info 'Default'] [VpxdVdb::SetDBType] Logging in to DSN: VMware vCenter with username
[04052 error 'Default'] [VpxKey::Decrypt] crypto failure: error:00000000:lib(0):func(0):reason(0)
[04052 error 'Default'] [VpxdCert] Failed to decrypt password: applying key to encrypted data failed (likely the wrong key)
[04052 error 'Default'] [VpxdVdb::SetDBType]: Database error: ODBC error: () -
[04052 error 'Default'] Error getting configuration info from the database
Looking through KB articles it would appear the issue is with the DB password and it requires re-authenticating. However, as I haven't got as far as loading the certificate into memory I don't understand why when I replace the old files with the newly created ones I get the error. After all the instructions state the DB password has to be re-entered once the new certificate has been loaded into memory.