Enemies can attack your clan Capital. However, they would first have to defeat all of the Forts defending it. You cannot send reinforcements to the Capital while it is protected by at least one Fort.

The Fort stops defending the Capital once it enters the state of Conflagration. Once under Conflagration, Fort’s Walls cannot be restored for the next 40 hours. If the Fort hosted allied reinforcements, then the Conflagration may or may not activate, depending on whether the enemy manages to defeat these reinforcements:

1. If the enemy defeated both Clan Walls and allied reinforcements at once, then Conflagration activates.
2. If the enemy only managed to defeat Clan Fortifications, then Conflagration does not activate while the destroyed defenses can be restored instantaneously.

If you charged the Capital Shield of Peace before the last Fort was defeated, then once the last Fort is under Conflagration, your Capital will be shielded for the next 20 hours. During this time allies can send reinforcements to the Capital. If an enemy manages to defeat both Capital Fortifications and allied reinforcements inside, she will take all clan resources stored in the Capital. You will not be able to restore Capital’s Walls unless you restore any Fort’s Walls first.

Note that upgrading a Fort during attack will not prevent its Conflagration in case of defeat.