The script for making your usb flash drive bootable with linux isos without lossing data.

mkmultibootusb.sh

#!/bin/bash
set -e
show_help () {
  cat <<EOF
The script for making multiboot linux live flashes.
Arguments:
  -b <path> 		set path to the boot directory on the flash drive
  -i <path to drive>	install loader to the suplied flash drive
  -a <path to iso>	add iso to multiboot flash
  -h 			show this help message
EOF
}

get_value() {
  local FIRSTWORDS=$(echo -e "$1" | grep -io "$2")
  if [ -z "$FIRSTWORDS" ]
  then
    return
  fi
  echo -e "$1" | sed -n "s/[ \\t]*$FIRSTWORDS[ \\t]*//gp"
}

unmount() {
  echo -n "Unmounting ISO file..."
  sudo umount $1
  rm -r $1
  echo "done"
}

convert_syslinux () {
local OLD_ISO_NAME=""
local NEW_ISO_NAME=""
local ISO_ROOT=""
local FLASH_ISO_ROOT=""
while [ $# -gt 1 ]
do
  case $1 in
    -oldisoname)
      OLD_ISO_NAME="$2"
      shift
      ;;
    -newisoname)
      NEW_ISO_NAME="$2"
      shift
      ;;
    -isoroot)
      ISO_ROOT="$2"
      shift
      ;;
    -flashisoroot)
      FLASH_ISO_ROOT="$2"
      shift
      ;;
    *)
      echo "Unknown option $1" >&2
      exit 1
      ;;
  esac
  shift
done 
local kernel=""
local initrd=""
local append=""
local label=""
local pre_label=""
local name=""
local line=""
read line
local the_end=1
#echo "---------- FILE STARTS -----------" >&2
while test $the_end
do
  read line
  the_end=$?
  append+=$(get_value "$line" '^[[:blank:]]*append' )
  kernel+=$(get_value "$line" '^[[:blank:]]*kernel'  )
  name+=$(  get_value "$line" '^[[:blank:]]*menu \+label')
  initrd+=$(get_value "$line" '^[[:blank:]]*initrd')
  label+=$( get_value "$line" '^[[:blank:]]*label')
  #echo "pre   =$pre_label" >&2
  #echo "label =$label" >&2
  #echo "append=$append" >&2
  #echo "kernel=$kernel" >&2
  if [ 1 -eq $the_end -o ! -z "$label" ]
  then
    if [ ! -z "$pre_label" ]
    then
      
      echo "menuentry \"$pre_label $name\" {"
      
      if [ -e "$ISO_ROOT/$kernel" -a ! -z "$kernel" ]
      then
        IFS=$' '
        local append_fixed=""
        for a in $append
        do
          local key=$(echo $a | sed -e 's/^\(.*\)=.*$/\1/')
          local val=$(echo $a | sed -n 's/^.*=\(.*\)$/\1/p')
          local newval=""
          if [ -z "$val" ]
          then
            newval=""
          elif [ "$OLD_ISO_NAME" = "$val" ]
          then
            newval="$NEW_ISO_NAME"
          elif [ -e "$ISO_ROOT/$val" ]
          then
            newval="/$FLASH_ISO_ROOT/$val"
          elif [ "$key" = "initrd" ]
          then
            if [ ! -z "$initrd" ]
            then
              initrd+=","
            fi
            initrd+="$val"
            continue
          else
            newval="$val"
          fi
          append_fixed+=" $key"
          if [ ! -z "$newval" ]
          then
            append_fixed+="=$newval"
          fi
        done
        echo "linux /$FLASH_ISO_ROOT/$kernel $append_fixed"
      fi
      if [ ! -z "$initrd" ]
      then
        local fixed_initrd=$(echo " $initrd" | sed -e 's/,/ /g' | sed -e "s% /% /$FLASH_ISO_ROOT/%g")
        echo "initrd $fixed_initrd"
      fi
      echo "}"
    fi
    pre_label="$label"
    label=""
    kernel=""
    append=""
    initrd=""
    name=""
  fi
done
}

while [ $# -gt 1 ]
do
  case $1 in
    -b)# Loader directory path
      BOOT_DIR="$2"
      shift
      ;;
    -i)# Install loader
      BOOT_DRIVE="$2"
      shift
      ;;
    -a)# Add iso
      ADD_ISO="$2"
      shift
      ;;
    -h)# Help
      show_help
      exit 0
      ;;
    *)
      echo "Unknown option $1"
      show_help
      exit 1
      ;;
  esac
  shift
done


IFS=$'\n'

if [ -z "$BOOT_DIR" ]
then
  echo "You need to specify a boot directory path on your flash drive, where loader files (have been/will be) installed!"
  show_help
  exit 1
fi

set +e
BOOT_DEV=$(df --output="source" "$BOOT_DIR" | grep '/dev')
GRUB_CONFIG="$BOOT_DIR/grub/grub.cfg"
#SYSLINUX_CONFIG="$BOOT_DIR/syslinux.cfg"
ISO_DIR="$BOOT_DIR/iso"
MOUNTED_FLASH=$(df --output="target" "$BOOT_DIR" | grep '/')

set -e
if [ ! -z "$BOOT_DRIVE" ]
then
  if [ ! -b "$BOOT_DRIVE" ]
  then
    echo "$BOOT_DRIVE is not a block device!"
    exit 1
  fi
  grub-install --boot-directory="$BOOT_DIR" "$BOOT_DRIVE"
  #syslinux --install --directory "$BOOT_DIR" "$BOOT_DEV"
fi

mkdir -p $ISO_DIR
if [ ! -z "$ADD_ISO" ]
then
  if [ ! -e "$ADD_ISO" ]
  then
    echo "File $ADD_ISO does not exist!"
    exit 1
  fi
  ISO_NAME=$(basename $ADD_ISO)
  MOUNTED_DIR=$(mktemp -d)
  THIS_ISO_DIR="$ISO_DIR/$ISO_NAME"

  echo "Mounting iso file..."
  mkdir -p "$MOUNTED_DIR"
  sudo mount -o ro "$ADD_ISO" "$MOUNTED_DIR"
  echo "Mounted!"
  
  ENTRIES=""
  ISO_CHROOT=$(realpath --relative-to=$MOUNTED_FLASH $THIS_ISO_DIR)
  NEWNAME=$(lsblk -n --output=LABEL $BOOT_DEV)
  LOOP_DEV=$(df --output="source" "$MOUNTED_DIR" | grep '/dev')
  OLDNAME=$(lsblk -n --output=LABEL $LOOP_DEV)
  if [ -z "$NEWNAME" -o -z "$OLDNAME" ]
  then
    echo "$NEWNAME old=$OLDNAME"
    echo "Error! Flash drives filesystem must have a label!" >&2
    unmount $MOUNTED_DIR
    exit 1
  fi
  echo -n "Searching for bootloader in ISO file..."
  CONFIGS=$(find "$MOUNTED_DIR" -name "isolinux.cfg" -or -name "syslinux.cfg")
  if [ ! -z "$CONFIGS" ]
  then
    mkdir -p "$THIS_ISO_DIR"
    echo "found ISOLINUX"
    echo -n "Generating entries..."
    for isoconfig in $CONFIGS
    do
      configpath=$(realpath --relative-to=$MOUNTED_DIR $isoconfig)
      mkdir -p $THIS_ISO_DIR/$(dirname $configpath)
#      cp $isoconfig $THIS_ISO_DIR/$configpath.fix
#      sed -i "s%\\([^a-z0-9_-]\\)/%\\1/$ISO_CHROOT/%g" $THIS_ISO_DIR/$configpath.fix
      #cat "$isoconfig" | convert_syslinux -isoroot "$MOUNTED_DIR" -flashisoroot "$ISO_CHROOT" -oldisoname "$OLDNAME" -newisoname "$NEWNAME"
      FIXED_CONFIG=$(cat "$isoconfig" | convert_syslinux -isoroot "$MOUNTED_DIR" -flashisoroot "$ISO_CHROOT" -oldisoname "$OLDNAME" -newisoname "$NEWNAME" | cat)
      ENTRIES+="
submenu \"$configpath\" 
{
  $FIXED_CONFIG
}
"
#      ENTRIES+="
#LABEL
#  MENU LABEL \"$configpath\"
#  CONFIG $ISO_CHROOT/$configpath.fix
#
#"
    done
    echo "done"
  else
    echo "not found"
  fi

  if [ ! -z "$ENTRIES" ]
  then
  
    echo -n "Copying content of iso file to the flash drive..."
    cp -Ru --target-directory="$THIS_ISO_DIR" $MOUNTED_DIR/*
    echo "done"

    cat > $THIS_ISO_DIR/subconfig.cfg << EOF
submenu "$ISO_NAME" {
$ENTRIES
}
EOF
  fi


  unmount $MOUNTED_DIR
  

fi

echo -n "Regenerating loader config..."
#SYSLINUX_INCLUDES=""
GRUB_INCLUDES=""

for iso in $(ls $ISO_DIR)
do
  if [ ! -e "$ISO_DIR/$iso/subconfig.cfg" ]
  then
    echo ""
    echo "skipping $iso"
    continue
  fi
  relpath=$(realpath --relative-to="$MOUNTED_FLASH" "$ISO_DIR/$iso")
  #if [ $(grep -c 'GRUB' $ISO_DIR/$iso/subconfig.cfg) -gt 0 ]
  #then
    GRUB_INCLUDES+="
menuentry \"$(basename $iso)\" {
  configfile (\$root)/$relpath/subconfig.cfg
}
"
#  else
#    SYSLINUX_INCLUDES+="
#LABEL
#  MENU LABEL \"$(basename $iso)\"
#  CONFIG $relpath/subconfig.cfg
#"
#  fi
done	
FSID=$(lsblk --output="UUID" -n "$BOOT_DEV")
cat > $GRUB_CONFIG << EOF
search --fs_uuid $FSID --set root
set gfxmode=auto
set gfxpayload=auto
insmod vbe
insmod gfxterm
terminal_output gfxterm
loadfont unicode
set lang=ru_RU

## ISO FILES ##
#menuentry "Syslinux based ISOs" {
#  chainloader (\$root)+1
#}
$GRUB_INCLUDES

EOF
#cat > $SYSLINUX_CONFIG << EOF
#$SYSLINUX_INCLUDES
#EOF

echo "done"