Enemies can attack your Clan Capital. Before doing so, however, they must first defeat all the Forts that are defending your Capital. You cannot send reinforcements to the Capital while it is protected by at least one Fort.

When a Fort acquires Conflagration status, it no longer protects the Capital, and the Fort's walls cannot be restored for the next 40 hours. If the Fort has allied reinforcements in it, then Conflagration status may or may not activate, depending on whether the enemy manages to defeat the reinforcements or not:

1. If the enemy eliminates the Clan Walls and the allied reinforcements, then Conflagration status activates.
2. If the enemy only manages to defeat the fortifications, then Conflagration status does not activate, and the destroyed defenses can be restored instantaneously.

If you charged the Capital's Shield of Peace before the last Fort was defeated, then when the last Fort becomes affected by Conflagration status, the Shield will activate for the next 20 hours. During this time, allies can send reinforcements to the Capital. 
If an enemy manages to overcome the Capital's fortifications and defeat the allied reinforcements inside, they will take all Clan resources stored in the Capital, regardless of their army's carrying capacity. You won't be able to restore the Capital's Walls unless you restore the Walls of any Fort first.

Note that upgrading a Fort during an attack will not prevent it from acquiring Conflagration status in case of a defeat. Forts that are being upgraded do not protect your Clan Capital. Placing an extra Fort while your Capital is under attack will not cancel the enemy march.