USB and SDCard stack fail when remove files

Question

Hi, 
 in our application we use SDCard and USB stack with the following configuration: 
 #Peripherals
CONFIG_GPIO=y
CONFIG_SPI=y
CONFIG_I2C=y
CONFIG_ADC=y
CONFIG_SERIAL=y
CONFIG_UART_INTERRUPT_DRIVEN=y

# Flash
CONFIG_FLASH=y
CONFIG_FLASH_PAGE_LAYOUT=y
CONFIG_MPU_ALLOW_FLASH_WRITE=y

CONFIG_PRINTK=y

CONFIG_LOG=y

# Infrared timer
CONFIG_COUNTER=y
CONFIG_COUNTER_RTC0=y
# This timer is used only for read IR competitor protocol
CONFIG_NRFX_TIMER1=y
CONFIG_NRFX_TIMER2=y

# SDCard & Filesystem
CONFIG_DISK_DRIVERS=y
CONFIG_DISK_DRIVER_SDMMC=y
CONFIG_DISK_ACCESS=y
CONFIG_FILE_SYSTEM=y
CONFIG_FAT_FILESYSTEM_ELM=y

# Bootloader
CONFIG_BOOTLOADER_MCUBOOT=y
CONFIG_IMG_MANAGER=y
CONFIG_MCUBOOT_IMG_MANAGER=y
#CONFIG_IMG_ERASE_PROGRESSIVELY=y

# Bluetooth configuration
CONFIG_BT=y
CONFIG_BT_OBSERVER=y
#CONFIG_BT_BROADCASTER=y
CONFIG_BT_HCI=y
# BT LE White list
CONFIG_BT_FILTER_ACCEPT_LIST=y

# Test filter by UUID
# CONFIG_BT_PERIPHERAL=y
# CONFIG_BT_CENTRAL=y
# CONFIG_BT_SCAN=y
# CONFIG_BT_SCAN_FILTER_ENABLE=y
# CONFIG_BT_SCAN_WITH_IDENTITY=y

# Accelerometer
# CONFIG_SENSOR=y
#CONFIG_LIS2DH=y
# +/- 2g
#CONFIG_LIS2DH_ACCEL_RANGE_2G=y
# 10Hz
#CONFIG_LIS2DH_ODR_2=y
# Low Power Mode - 8bit
#CONFIG_LIS2DH_OPER_MODE_LOW_POWER=y

# Enable Low Power
CONFIG_PM=y
CONFIG_PM_DEVICE=y
CONFIG_REBOOT=y

#USB related configs
CONFIG_USB_DEVICE_STACK=y
CONFIG_USB_DEVICE_PRODUCT="SGuide V3"
CONFIG_USB_DRIVER_LOG_LEVEL_ERR=y
CONFIG_USB_MASS_STORAGE=y
CONFIG_USB_DEVICE_LOG_LEVEL_ERR=y
CONFIG_USB_MASS_STORAGE_LOG_LEVEL_ERR=y
CONFIG_APP_MSC_STORAGE_SDCARD=y
#CONFIG_USB_DEVICE_PID=0x0008

# Used on AM131 Board
CONFIG_NFCT_PINS_AS_GPIOS=y
CONFIG_BOARD_ENABLE_DCDC_APP=n
CONFIG_BOARD_ENABLE_DCDC_NET=n
CONFIG_BOARD_ENABLE_DCDC_HV=n
CONFIG_CLOCK_CONTROL_NRF_K32SRC_RC=n
CONFIG_CLOCK_CONTROL_NRF_K32SRC_XTAL=y

# Other 
CONFIG_MAIN_STACK_SIZE=8192
CONFIG_IDLE_STACK_SIZE=4096

CONFIG_SIZE_OPTIMIZATIONS=n

# Reset on hard fault
CONFIG_RESET_ON_FATAL_ERROR=y 
 The communication with the nRF5340 is done by using a Linux Embedded systems. When the device is connected to Linux, I copy a folder inside the SDCard without any problem. 
 When I remove the folder and put into a new one the copy fails and the linux systems told us that the memory was corrupted. 
 Instead, if I remove the folder directly from the OS (by removing the SDCard from the board with the nRF5340), and after that I write the folder by using the nRF5340 it works correctly. 
 The device are in production and we don't know how solve this issue!! Can you help us? 
 Best 
 Marco