Is it possible to migrate certificates and upgrade the version of Symantec Critical Systems Protection 5.2.9 to DCS 6.x in the same step?
You cannot migrate certificates and upgrade the version of SCSP to DCS in the same step. The server.exe installer needs to create the new server.xml against your certificates. The reason is that 5.2.9 certificates are in JKS format and DCS 6.5 certificates use PKCS12; therefore, the keystoretype will not match.
The server.exe installer must create the new server.xml against your certificates, which is by design.