A few thoughts about the code you posted at the beginning of this topic:
Line 24: Comment is wrong
Line 29: You select MCK/32 whith TC_CMR_TCCLKS_TIMER_CLOCK3, so final frequency is 84000000/32/400 = 6562 Hz, is this what you want ?
There is something I guess is wrong in your sketch : Let's say you exit from TC1_Handler() with num_buff_lec = 0 and auto_remp_buffer = 1, then in loop() you enter the first if() condition, then the second if() condition to fill buffer1. Next time when you enter TC1_Handler(),num_buff_lec = 0 so you should work with the previous buffer you filled, namely buffer1 NOT buffer0 !!
At some point, if you increase the timer frequency, you will fill a first buffer slower in loop() than you will leverage the other one in TC_Handler() because of the SD card reading speed.