diff --git a/anyio.c b/anyio.c
index 7cf96df..11378e4 100644
--- a/anyio.c
+++ b/anyio.c
@@ -205,7 +205,7 @@ board_t *anyio_get_dev(board_access_t *access, int board_number) {
     return NULL;
 }
 
-int anyio_dev_write_flash(board_t *board, char *bitfile_name, int fallback_flag) {
+int anyio_dev_write_flash(board_t *board, char *bitfile_name, int fallback_flag, int fix_boot_flag) {
     int ret;
 
     if (board == NULL) {
@@ -217,7 +217,7 @@ int anyio_dev_write_flash(board_t *board, char *bitfile_name, int fallback_flag)
         if (fallback_flag == 1) {
             addr = FALLBACK_ADDRESS;
         }
-        ret = board->llio.write_flash(&(board->llio), bitfile_name, addr);
+        ret = board->llio.write_flash(&(board->llio), bitfile_name, addr, fix_boot_flag);
     } else {
         printf("ERROR: Board %s doesn't support flash writing.\n", board->llio.board_name);
         return -EINVAL;
diff --git a/anyio.h b/anyio.h
index b804e51..1cad7fe 100644
--- a/anyio.h
+++ b/anyio.h
@@ -29,7 +29,7 @@ int anyio_init(board_access_t *access);
 void anyio_cleanup(board_access_t *access);
 int anyio_find_dev(board_access_t *access);
 board_t *anyio_get_dev(board_access_t *access, int board_number);
-int anyio_dev_write_flash(board_t *board, char *bitfile_name, int fallback_flag);
+int anyio_dev_write_flash(board_t *board, char *bitfile_name, int fallback_flag, int fix_boot_flag);
 int anyio_dev_verify_flash(board_t *board, char *bitfile_name, int fallback_flag);
 int anyio_dev_program_fpga(board_t *board, char *bitfile_name);
 int anyio_dev_set_remote_ip(board_t *board, char *lbp16_set_ip_addr);
diff --git a/eeprom.c b/eeprom.c
index 40a86d9..bb04e39 100644
--- a/eeprom.c
+++ b/eeprom.c
@@ -149,7 +149,7 @@ int start_programming(llio_t *self, u32 start_address, int fsize) {
     return 0;
 }
 
-int eeprom_write(llio_t *self, char *bitfile_name, u32 start_address) {
+int eeprom_write(llio_t *self, char *bitfile_name, u32 start_address, int fix_boot_flag) {
     board_t *board = self->board;
     int bytesread, i;
     u32 eeprom_addr;
@@ -184,15 +184,21 @@ int eeprom_write(llio_t *self, char *bitfile_name, u32 start_address) {
 // if board doesn't support fallback there is no boot block
     if (board->fallback_support == 1) {
         if (check_boot(self) == -1) {
-            write_boot(self);
+            if (fix_boot_flag) {
+                write_boot(self);
+                if (check_boot(self) == -1) {
+                    printf("Failed to write valid boot sector\n");
+                    fclose(fp);
+                    return -1;
+                }
+            } else {
+                printf("Error: BootSector is invalid\n");
+                fclose(fp);
+                return -1;
+            }
         } else {
             printf("Boot sector OK\n");
         }
-        if (check_boot(self) == -1) {
-            printf("Failed to write valid boot sector\n");
-            fclose(fp);
-            return -1;
-        }
     }
 
     if (eeprom_access.start_programming(self, start_address, file_stat.st_size) == -1) {
diff --git a/eeprom.h b/eeprom.h
index 2ffc8fb..8adef37 100644
--- a/eeprom.h
+++ b/eeprom.h
@@ -55,7 +55,7 @@ char *eeprom_get_flash_type(u8 flash_id);
 u32 eeprom_calc_user_space(u8 flash_id);
 void eeprom_prepare_boot_block(u8 flash_id);
 int start_programming(llio_t *self, u32 start_address, int fsize);
-int eeprom_write(llio_t *self, char *bitfile_name, u32 start_address);
+int eeprom_write(llio_t *self, char *bitfile_name, u32 start_address, int fix_boot_flag);
 int eeprom_verify(llio_t *self, char *bitfile_name, u32 start_address);
 void eeprom_init(llio_t *self);
 void eeprom_cleanup(llio_t *self);
diff --git a/eeprom_local.c b/eeprom_local.c
index e7467c7..d13b809 100644
--- a/eeprom_local.c
+++ b/eeprom_local.c
@@ -419,10 +419,10 @@ static void done_programming(llio_t *self) {
 
 // global functions
 
-int local_write_flash(llio_t *self, char *bitfile_name, u32 start_address) {
+int local_write_flash(llio_t *self, char *bitfile_name, u32 start_address, int fix_boot_flag) {
     int ret;
 
-    ret = eeprom_write(self, bitfile_name, start_address);
+    ret = eeprom_write(self, bitfile_name, start_address, fix_boot_flag);
     done_programming(self);
     return ret;
 }
diff --git a/eeprom_local.h b/eeprom_local.h
index 36eceeb..62c5482 100644
--- a/eeprom_local.h
+++ b/eeprom_local.h
@@ -44,7 +44,7 @@
 #define EPP_SPI_SREG_REG      0x7E
 
 u8 read_flash_id(llio_t *self);
-int local_write_flash(llio_t *self, char *bitfile_name, u32 start_address);
+int local_write_flash(llio_t *self, char *bitfile_name, u32 start_address, int fix_boot_flag);
 int local_verify_flash(llio_t *self, char *bitfile_name, u32 start_address);
 void open_spi_access_local(llio_t *self);
 void close_spi_access_local(llio_t *self);
diff --git a/eeprom_remote.c b/eeprom_remote.c
index b95700c..d003811 100644
--- a/eeprom_remote.c
+++ b/eeprom_remote.c
@@ -91,8 +91,8 @@ static int remote_start_programming(llio_t *self, u32 start_address, int fsize)
 
 // global functions
 
-int remote_write_flash(llio_t *self, char *bitfile_name, u32 start_address) {
-    return eeprom_write(self, bitfile_name, start_address);
+int remote_write_flash(llio_t *self, char *bitfile_name, u32 start_address, int fix_boot_flag) {
+    return eeprom_write(self, bitfile_name, start_address, fix_boot_flag);
 }
 
 int remote_verify_flash(llio_t *self, char *bitfile_name, u32 start_address) {
diff --git a/eeprom_remote.h b/eeprom_remote.h
index e2a1e99..2884d44 100644
--- a/eeprom_remote.h
+++ b/eeprom_remote.h
@@ -21,7 +21,7 @@
 
 #include "hostmot2.h"
 
-int remote_write_flash(llio_t *self, char *bitfile_name, u32 start_address);
+int remote_write_flash(llio_t *self, char *bitfile_name, u32 start_address, int fix_boot_flag);
 int remote_verify_flash(llio_t *self, char *bitfile_name, u32 start_address);
 void open_spi_access_remote(llio_t *self);
 void close_spi_access_remote(llio_t *self);
diff --git a/hostmot2.h b/hostmot2.h
index 0dcbcc8..984f935 100644
--- a/hostmot2.h
+++ b/hostmot2.h
@@ -52,7 +52,7 @@ typedef struct {
 struct llio_struct {
     int (*read)(llio_t *self, u32 addr, void *buffer, int size);
     int (*write)(llio_t *self, u32 addr, void *buffer, int size);
-    int (*write_flash)(llio_t *self, char *bitfile_name, u32 start_address);
+    int (*write_flash)(llio_t *self, char *bitfile_name, u32 start_address, int fix_boot_flag);
     int (*verify_flash)(llio_t *self, char *bitfile_name, u32 start_address);
     int (*program_fpga)(llio_t *self, char *bitfile_name);
     int (*reset)(llio_t *self);
diff --git a/mesaflash.c b/mesaflash.c
index af66837..f528690 100644
--- a/mesaflash.c
+++ b/mesaflash.c
@@ -33,6 +33,7 @@ static int device_flag;
 static int addr_flag;
 static int addr_hi_flag;
 static int write_flag;
+static int fix_boot_flag;
 static int verify_flag;
 static int fallback_flag;
 static int recover_flag;
@@ -63,6 +64,7 @@ static struct option long_options[] = {
     {"addr", required_argument, 0, 'a'},
     {"addr_hi", required_argument, 0, 'b'},
     {"write", required_argument, 0, 'w'},
+    {"fix-boot-block", no_argument, &fix_boot_flag, 1},
     {"verify", required_argument, 0, 'v'},
     {"fallback", no_argument, &fallback_flag, 1},
     {"recover", no_argument, &recover_flag, 1},
@@ -122,6 +124,7 @@ void print_usage() {
     printf("  --verbose     print detailed information while running commands\n");
     printf("\nCommands:\n");
     printf("  --write       writes a standard bitfile 'filename' configuration to the userarea of the EEPROM (IMPORTANT! 'filename' must be VALID FPGA configuration file)\n");
+    printf("      --fix-boot-block  If a write operation does not detect a valid boot block, write one\n");
     printf("  --verify      verifies the EEPROM configuration against the bitfile 'filename'\n");
     printf("  --program     writes a standard bitfile 'filename' configuration to the FPGA (IMPORTANT! 'filename' must be VALID FPGA configuration file)\n");
     printf("  --readhmid    print hostmot2 configuration in PIN file format\n");
@@ -373,7 +376,7 @@ int main(int argc, char *argv[]) {
         } else if (set_flag == 1) {
             ret = anyio_dev_set_remote_ip(board, lbp16_set_ip_addr);
         } else if (write_flag == 1) {
-            ret = anyio_dev_write_flash(board, bitfile_name, fallback_flag);
+            ret = anyio_dev_write_flash(board, bitfile_name, fallback_flag, fix_boot_flag);
             if (ret == 0)
             {
                 if (reload_flag == 1) {