Complex sentence: For the very brief period that Aury controlled Amelia Island, the flag of the revolutionary Republic of Mexico was flown, which was the flag of his clients who were still fighting the Spanish in their war for independence at that time.
Split into simpler sentences: For the very brief period that Aury controlled Amelia Island, the flag of the revolutionary Republic of Mexico was flown. This was the flag of his clients who were still fighting the Spanish in their war for independence at that time.