Does SPF remove some lines of header?

It's not possible for any policy server to cause that to happen. All it can do is cause a message to be rejected, deferred, or accepted and if accepted have a new header field added. I don't know what is causing your problem, but the interface we use with postfix does not permit that kind of modification.

Thank you for your answer.
Though, I found the only difference between removed or not is on / off of SPF module.
If I comment out
    policy-spf unix - n n - 0 spawn
      user=nobody argv=/usr/bin/python /usr/bin/policyd-spf /etc/python-policyd-spf/policyd-spf.conf
from master.cf, and
    smtpd_recipient_restrictions = permit_mynetworks,permit_sasl_authenticated,reject_unauth_destination,check_policy_service unix:private/policy-spf
    policy-spf_time_limit = 3600
from main.cf, the header won't be removed.

I'm really got in trouble. I know that it shouldn't be removed by SPF module, but it is removed.
Could you please give me an idea?

It's not just that it shouldn't be, it can't be. The interface that the policy server uses can't remove header fields. You are using a really old version of postfix. You might check if there are any related changes in a later version.