Fixed upstream:
master: https://fedorahosted.org/freeipa/changeset/610594156eafee2d0ced3a4d0484e4436b6f973d
ipa-3-0: https://fedorahosted.org/freeipa/changeset/f3ebc61b4926de837eb8ce80a10d24ba17b021ae

Reproducer:
1) Install IPA server with global forwarder configured:
# ipa-server-install --setup-dns --forwarder $FORWARDER_IP

2) Create a zone and delegate its sub-zone to other name server (which may be for example IPA server with IP 10.0.0.2)

# ipa dnszone-add example.com
# ipa dnsrecord-add example.com ns.sub --a-rec=10.0.0.2  # IP address of second IPA server with configured sub.example.com zone
# ipa dnsrecord-add example.com sub --ns-rec=ns.sub.example.com.

On second IPA server (with IP 10.0.0.2)
# ipa dnszone-add sub.example.com --nameserver ns --ip-address 10.0.0.2
# ipa dnsrecord-add sub.example.com client --a-rec 10.0.0.5

3) When you try to resolve client.sub.example.com on the first IPA server, the request will be routed through $FORWARDER_IP. You can verify that for example with tcpdump run on the first IPA server machine:

# tcpdump -ni eth0 udp port 53

4) Now, when you update the forwarders for example.com to "none", request for client.sub.example.com should go directly to second IPA server (i.e. 10.0.0.2)

# ipa dnszone-mod example.com --forwarder=none
# host client.sub.example.com

Web UI part fixed upstream:
 * ipa-3-0: 7f9d3dc3ddf41cfaeeedf83f669c852032f29549
 * master: 1bf537db9e6e5a66a7c3ce58019693098ff090f7

I am able to make it work using a alternate set of directions listed below, the steps to reproduce from above aren't quite right.

The IP address of zippyvm11 is 10.14.5.226
The IP address of zippyvm4 is 10.14.5.136

[root@zippyvm4 ~]# ipa dnszone-add example.com --name-server=zippyvm4.testrelm.com. --admin-email=hostmaster.example.com.
  Zone name: example.com
  Authoritative nameserver: zippyvm4.testrelm.com.
  Administrator e-mail address: hostmaster.example.com.
  SOA serial: 1358895286
  SOA refresh: 3600
  SOA retry: 900
  SOA expire: 1209600
  SOA minimum: 3600
  BIND update policy: grant TESTRELM.COM krb5-self * A; grant TESTRELM.COM
                      krb5-self * AAAA; grant TESTRELM.COM krb5-self * SSHFP;
  Active zone: TRUE
  Dynamic update: FALSE
  Allow query: any;
  Allow transfer: none;


[root@zippyvm4 ~]#  ipa dnsrecord-add example.com ns.sub --a-rec=10.14.5.226
  Record name: ns.sub
  A record: 10.14.5.226

[root@zippyvm4 ~]# ipa dnsrecord-add example.com sub --ns-rec=ns.sub.example.com.
  Record name: sub
  NS record: ns.sub.example.com.

[root@zippyvm4 ~]# ipa dnszone-mod --forwarder=10.14.5.226 example.com
  Zone name: example.com
  Authoritative nameserver: zippyvm4.testrelm.com.
  Administrator e-mail address: hostmaster.example.com.
  SOA serial: 1358895375
  SOA refresh: 3600
  SOA retry: 900
  SOA expire: 1209600
  SOA minimum: 3600
  Active zone: TRUE
  Allow query: any;
  Allow transfer: none;
  Zone forwarders: 10.14.5.226

[root@zippyvm11 ~]# ipa dnszone-add sub.example.com --name-server zippyvm11.testrelm.com.
Administrator e-mail address [hostmaster.sub.example.com.]: 
  Zone name: sub.example.com
  Authoritative nameserver: zippyvm11.testrelm.com.
  Administrator e-mail address: hostmaster.sub.example.com.
  SOA serial: 1358896319
  SOA refresh: 3600
  SOA retry: 900
  SOA expire: 1209600
  SOA minimum: 3600
  BIND update policy: grant TESTRELM.COM krb5-self * A; grant TESTRELM.COM krb5-self * AAAA; grant TESTRELM.COM krb5-self * SSHFP;
  Active zone: TRUE
  Dynamic update: FALSE
  Allow query: any;
  Allow transfer: none;

[root@zippyvm11 ~]# ipa dnsrecord-add sub.example.com client --a-rec 10.14.5.226
  Record name: client
  A record: 10.14.5.226

[root@zippyvm4 ~]# dig client.sub.example.com
; <<>> DiG 9.8.2rc1-RedHat-9.8.2-0.16.rc1.el6 <<>> client.sub.example.com
;; global options: +cmd
;; Got answer:
;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 40603
;; flags: qr rd ra; QUERY: 1, ANSWER: 1, AUTHORITY: 1, ADDITIONAL: 1

;; QUESTION SECTION:
;client.sub.example.com.		IN	A

;; ANSWER SECTION:
client.sub.example.com.	86400	IN	A	10.14.5.226

;; AUTHORITY SECTION:
sub.example.com.	86400	IN	NS	zippyvm11.testrelm.com.

;; ADDITIONAL SECTION:
zippyvm11.testrelm.com.	1200	IN	A	10.14.5.226

;; Query time: 15 msec
;; SERVER: 10.14.5.136#53(10.14.5.136)
;; WHEN: Tue Jan 22 18:14:48 2013
;; MSG SIZE  rcvd: 105

[root@zippyvm4 ~]# ipa dnszone-mod example.com --forwarder=
  Zone name: example.com
  Authoritative nameserver: zippyvm4.testrelm.com.
  Administrator e-mail address: hostmaster.example.com.
  SOA serial: 1358896093
  SOA refresh: 3600
  SOA retry: 900
  SOA expire: 1209600
  SOA minimum: 3600
  Active zone: TRUE
  Allow query: any;
  Allow transfer: none;
[root@zippyvm4 ~]# dig client.sub.example.com

; <<>> DiG 9.8.2rc1-RedHat-9.8.2-0.16.rc1.el6 <<>> client.sub.example.com
;; global options: +cmd
;; Got answer:
;; ->>HEADER<<- opcode: QUERY, status: NXDOMAIN, id: 19492
;; flags: qr rd ra; QUERY: 1, ANSWER: 0, AUTHORITY: 0, ADDITIONAL: 0

;; QUESTION SECTION:
;client.sub.example.com.		IN	A

;; Query time: 93 msec
;; SERVER: 10.14.5.136#53(10.14.5.136)
;; WHEN: Tue Jan 22 18:15:26 2013
;; MSG SIZE  rcvd: 40


I do seem to be able to remove the per-zone forwarder.

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory, and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

http://rhn.redhat.com/errata/RHSA-2013-0528.html