Step 1 For M3K player make sure you have the stored serial number of the device (usually on package box), you can also find it in the Settings section player "About device" / "About M3"
For M5 player, write down the current Bluetooth MAC-address of the player and the serial number of the device in a notebook, you can see them in the section "About the device" / "About M5"
Step 2 Install USB drivers for the device from the directory "\cloner-win32-driver"
Disable driver signature enforcement in the Windows boot parameters before that step. It takes effect only once until the next reboot.
Alternatively you can try to install WinUSB driver with Zadig
https://forums.rockbox.org/index.php/topic,53858.0.html (need to confirm)
Installing driver guide is not major topic of this recovery guide so here are few pictures just for reference.
Step 3 Run application "USB Cloner Tool" on the path "\cloner-2.5.0-windows_release\cloner.exe"
Step 4 Press on Config button
Step 5 In "INFO" tab choose "x1000" in "Platform" field and specific configuration file in "Boad" field.
FiiO M3K device needs "M3K_x1000_sfc_nand_lpddr_recovery.cfg"
FiiO M5 device needs "M5_x1000_sfc_nand_lpddr_recovery.cfg"
Step 6 Go to "POLICY" tab and set the paths to every firmware part files.
You may find the needed parts of full firmware version 1.2 on "\M3K_firmware_1.2" and "\M5_firmware_1.2" directories.
for example
uboot = ...\x-loader-pad-with-sleep-lib.bin
xImage = ...\xImage
recovery = ...\recovery
system = ...\system.ubi
data = ...\data.ubi
Generally you do not need to choose all of parts and can set and choose only that you need to flash/update.
I.e. if you have extracted parts from "ota update" firmware v1.4.5 it provides only bootloader, kernel image and system partition image.
Here are example of configuration that will flash/update all selected parts
for M3K
and M5 player device
Attention! It's very important to note that there is the check box "Erase All" that sets by default in "SFC" tab. It allows to erase all internal FLASH memory.
So if you do not need to erase all of internal memory content unset that checkbox.
Step 7 You may save tool's settings but make sure that path to configuration file should not contain the spaces.
Step 8 Make sure that player does not connected to PC and press "Start" button in the tool.
Now make sure that player powered off then press "Volume-" button on the player and connect the player to PC with USB cable. The firmware flashing starts.

After successful firmware update the player will reboot automatically.
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Here are USB driver, "USB cloner tool" and firmware v1.2 for FiiO M3K and M5 players.
Download link: https://www.mediafire.com/file/exzvvxjp4l3ai8u/M3K_M5_USB_cloner_tool.zip/file