While committing any changes on the master RE and configuration is in "protected" mode, the config is not synchronised and change is not reflected on backup RE.
Example:
Master:
labroot@jtac-mx480-r2013-re0> show system rollback compare 0 3
[edit interfaces ae10]
+ protect: unit 963 {
+ description "[106312269][CORP][ILL][VNM-VL3651][TOA HTC-HOALAC]";
+ vlan-id 963;
+ family inet {
+ filter {
+ output ILL-VNM-VL3651;
+ }
+ address 113.20.96.77/30;
+ family inet6 {
+ address 2402:5300:404:a::/127;
{master}
labroot@jtac-mx480-r2013-re0> show configuration | display set | count
Count: 37701 lines
labroot@jtac-mx480-r2013-re0> show configuration interfaces ae10 unit 963| display set
Backup:
{backup}
labroot@jtac-mx480-r2013-re1> show configuration | display set | count
Count: 37707 lines
labroot@jtac-mx480-r2013-re1> show configuration interfaces ae10 unit 963 | display set
set interfaces ae10 unit 963 description "[106312269][CORP][ILL][VNM-VL3651][TOA HTC-HOALAC]"
set interfaces ae10 unit 963 vlan-id 963
set interfaces ae10 unit 963 family inet filter output ILL-VNM-VL3651
set interfaces ae10 unit 963 family inet address 113.20.96.77/30
set interfaces ae10 unit 963 family inet6 address 2402:5300:404:a::/127
protect interfaces ae10 unit 963
As per current behaviour, first "unprotect" the config/interface in first commit and later modify the config in next commit.
When "unprotect" and config change both are done in single commit then "unprotect" is NOT sent to backup RE and hence this behaviour is observed where configuration gets out-of-sync with backup RE.