[Xiaomi Redmi Note 3 Questions & Answers] Amon_Re:
Just doublechecked: Persist is already in there:

<partition label="persist" size_in_kb="32768" type="6C95E238-E343-4BA8-B489-8681ED22AD0B" bootable="false" readonly="false" filename="persist.img" sparse="true"/>

Just doublechecked the logfile for Mi Flash (After I flashed in EDL mode, not in fastboot mode) and it was flashed:

[15:50:39 COM20]:Write sparse file D:\kate_global_images_9.3.28_20190328.0000.00_6.0_global\images\persist.img to partition[persist] sector 7995392
[15:50:39 COM20]:total chunks 14, current chunk 1
[15:50:39 COM20]:write file legnth 4829380 to partition 7995392
[15:50:39 COM20]:WriteFile position 0, size 4096
[15:50:39 COM20]:total chunks 14, current chunk 2
[15:50:39 COM20]:write file legnth 4829380 to partition 7995400
[15:50:39 COM20]:WriteFile position 1000, size 4096
[15:50:39 COM20]:total chunks 14, current chunk 3
[15:50:39 COM20]:write file legnth 4829380 to partition 7995408
[15:50:39 COM20]:WriteFile position 2000, size 28672
[15:50:39 COM20]:total chunks 14, current chunk 4
[15:50:39 COM20]:write file legnth 4829380 to partition 7995464
[15:50:39 COM20]:WriteFile position 9000, size 8192
[15:50:39 COM20]:total chunks 14, current chunk 5
[15:50:39 COM20]:write file legnth 4829380 to partition 7995480
[15:50:39 COM20]:WriteFile position B000, size 131072
[15:50:39 COM20]:WriteFile position 2B000, size 131072
[15:50:39 COM20]:WriteFile position 4B000, size 131072
[15:50:39 COM20]:WriteFile position 6B000, size 131072
[15:50:39 COM20]:total chunks 14, current chunk 6
[15:50:39 COM20]:write file legnth 4829380 to partition 7996504
[15:50:39 COM20]:WriteFile position 8B000, size 131072
[15:50:40 COM20]:WriteFile position AB000, size 131072
[15:50:40 COM20]:WriteFile position CB000, size 131072
[15:50:40 COM20]:WriteFile position EB000, size 131072
[15:50:40 COM20]:WriteFile position 10B000, size 131072
[15:50:40 COM20]:WriteFile position 12B000, size 131072
[15:50:40 COM20]:WriteFile position 14B000, size 131072
[15:50:40 COM20]:WriteFile position 16B000, size 131072
[15:50:40 COM20]:WriteFile position 18B000, size 131072
[15:50:40 COM20]:WriteFile position 1AB000, size 131072
[15:50:40 COM20]:WriteFile position 1CB000, size 131072
[15:50:40 COM20]:WriteFile position 1EB000, size 131072
[15:50:40 COM20]:WriteFile position 20B000, size 131072
[15:50:40 COM20]:WriteFile position 22B000, size 131072
[15:50:40 COM20]:WriteFile position 24B000, size 131072
[15:50:40 COM20]:WriteFile position 26B000, size 131072
[15:50:40 COM20]:WriteFile position 28B000, size 131072
[15:50:40 COM20]:WriteFile position 2AB000, size 131072
[15:50:40 COM20]:WriteFile position 2CB000, size 131072
[15:50:40 COM20]:WriteFile position 2EB000, size 131072
[15:50:40 COM20]:WriteFile position 30B000, size 131072
[15:50:40 COM20]:WriteFile position 32B000, size 131072
[15:50:40 COM20]:WriteFile position 34B000, size 131072
[15:50:40 COM20]:WriteFile position 36B000, size 131072
[15:50:40 COM20]:WriteFile position 38B000, size 131072
[15:50:40 COM20]:WriteFile position 3AB000, size 131072
[15:50:40 COM20]:WriteFile position 3CB000, size 131072
[15:50:40 COM20]:WriteFile position 3EB000, size 131072
[15:50:40 COM20]:WriteFile position 40B000, size 131072
[15:50:41 COM20]:WriteFile position 42B000, size 131072
[15:50:41 COM20]:WriteFile position 44B000, size 131072
[15:50:41 COM20]:WriteFile position 46B000, size 131072
[15:50:41 COM20]:total chunks 14, current chunk 7
[15:50:41 COM20]:write file legnth 4829380 to partition 8004696
[15:50:41 COM20]:WriteFile position 48B000, size 4096
[15:50:41 COM20]:total chunks 14, current chunk 8
[15:50:41 COM20]:write file legnth 4829380 to partition 8004704
[15:50:41 COM20]:WriteFile position 48C000, size 4096
[15:50:41 COM20]:total chunks 14, current chunk 9
[15:50:41 COM20]:write file legnth 4829380 to partition 8004712
[15:50:41 COM20]:WriteFile position 48D000, size 4096
[15:50:41 COM20]:total chunks 14, current chunk 10
[15:50:41 COM20]:write file legnth 4829380 to partition 8004720
[15:50:41 COM20]:WriteFile position 48E000, size 32768
[15:50:41 COM20]:10 chunks match 20 ack
[15:50:41 COM20]:total chunks 14, current chunk 11
[15:50:41 COM20]:write file legnth 4829380 to partition 8004784
[15:50:41 COM20]:WriteFile position 496000, size 12288
[15:50:41 COM20]:total chunks 14, current chunk 12
[15:50:41 COM20]:write file legnth 4829380 to partition 8004808
[15:50:41 COM20]:WriteFile position 499000, size 4096
[15:50:41 COM20]:total chunks 14, current chunk 13
[15:50:41 COM20]:write file legnth 4829380 to partition 8004816
[15:50:41 COM20]:WriteFile position 49A000, size 4096
[15:50:41 COM20]:total chunks 14, current chunk 14
[15:50:41 COM20]:3 chunks match 6 ack
[15:50:41 COM20]:Image D:\kate_global_images_9.3.28_20190328.0000.00_6.0_global\images\persist.img transferred successfully

The partition determinately was written, at this point I can only conclude that it's dead