To follow up on Ziggy's question, and on the issue reported by Nacey:
Your guild will be unregistered from war when you have less then 10 members opted in, or LESS THAN 50% OF YOUR MEMBERS (whichever number is higher).
In the case of MSA Elite on S4 this seems to have been the case, as they opted out more than half their members from war.
This rule was in place even before the 2.12 changes, but I assume this issue is now hitting more guilds because:
a) In game versions earlier than 2.12 a guild could enter the running war again when they opted enough members back in, at least if they were unregistered due to the 10 member minimum opt in threshold.
b) Since opting out affects guild members longer, there end up longer periods of time with less members being opted in without a possibility to quickly opt a member back in to make up for it immediately. So this might now affect guilds that hadn't experienced this before, as they always had at least 50% of members opted in during the course of war.