To check the symptoms or error logs it's always recommend to have a backup of the configuration, however Netscaler has it's last 5 saved configuration by default under /nsconfig/ directory.

Compare the directory for the changes after the reboot/failover or build upgrade.

Also to check why the VLAN binding is missing check the /var/nssynclog directory logs for sync_batch_status.log file. It will have an output for the command executed to sync the Netscaler configuration for the remote HA pair.

The status of the executed commands can be seen as below:

You can refer the commands which got executed with status and the reason for any failure will also be visible in the results.
For Example: In above screenshot VLAN binding to interface got failed as there was no LA/3 interface was present. 

Ensure that LA channel configuration is identical on both HA pairs.

Problem Cause

The VLAN configuration went missing is because of the LA interface has different -lakeys(LA/3 and LA/7) in the VPX/MPX’s. During the HA sync where the VLAN binding sync was initiated but failed as NetScaler was not able to find out the Exact LA channel number(LA/3) on itself and thus the VLAN sync failed and VLAN binding went missing.