Well, it seems like the update already happened, despite that bad message.

SBUU recognised the repository exported to USB key in SUU format and firmwares where already updated.

I just want to write down the two procedures just in case anybody else needs help:

How do you update a PE Server using only USB (No DVD drive)?

Using SBUU and Repository manager

First Phase: SBUU

1. Download the propoer SBUU dvd ISO from dell support site
2. Mount it on your linux distro (I used Centos 6). It's important to have an installed distro with grub, cause it'll look for that.
3. Check if unetinfo command is installed to your system. If it is, jump to 7. [ 99%, if you are using a recent distro, it'll not. You'll have instead unetadm command.]
4. run su command and insert root passwd to act as root user
5. copy this file on your desktop: mount_path/server_assistant/driver_tool/src/make_bootable_usb.sh
6. open it with a plain text editor (like vi) and replace all the occurrences of unetinfo command with unetadm info
7. Apply execute permission to the file
8. Insert your USB drive
9. run ./make_bootable_usb.sh --scan and check if it sees your USB stick.
10. unmount it (just unmount, not eject)
11. run ./make_bootable_usb.sh /path_to_mounted_iso /path_to_usb 

Ex:

[user@localhost /]# su

[root@localhost /]# mount -o loop /home/user/SBUU.iso /mnt/SBUU

[root@localhost /]# cp /mnt/SBUU/server_assistant/driver_tool/src/make_bootable_usb.sh /home/user/Desktop

[root@localhost /]# vi /home/user/Desktop/make_bootable_usb.sh (

[root@localhost Desktop]# ./make_bootable_usb.sh --scan

Usage Note:

This is a sample script:
The following commands/rpm should be installed for the tool to work:
udevinfo, mtools, parted, (minimum version required is 1.6.25.1), grub-install (grub), and lsusb. Please ensure they are available on the system. If not,
please edit the scripts accordingly

USB 1 ( Device : /dev/sdb): Generic

[root@localhost Desktop]# ./make_bootable_usb.sh /media/SBUU /dev/sdb

Usage Note:

This is a sample script:
The following commands/rpm should be installed for the tool to work:
udevinfo, mtools, parted, (minimum version required is 1.6.25.1), grub-install (grub), and lsusb. Please ensure they are available on the system. If not,
please edit the scripts accordingly

All the data in /dev/sdb will be erased!! Continue ? [N/y]
y
Completed Clearing USB Drive
WARNING: you are attempting to use parted to operate on (mkpartfs) a file system.
parted's file system manipulation code is not as robust as what you'll find in
dedicated, file-system-specific packages like e2fsprogs. We recommend
you use parted only to manipulate partition tables, whenever possible.
Support for performing most operations on most types of file systems
will be removed in an upcoming release.
Created Single USB Partition /dev/sdb1
Copying files....
Installation finished. No error reported.
This is the contents of the device map /tmp/tmp.QRt9hm6Z4T/boot/grub/device.map.
Check if this is correct or not. If any of the lines is incorrect,
fix it and re-run the script `grub-install'.

(hd0) /dev/sdb
Unmounting USB device
Process Completed!..

Now you'll have SBUU installed and bootable on your USB Stick

Second Phase: Update Repository

Next step is to download and install Dell Repository Manager on a Windows machine.

(Note: I used VM both for Win7 a Centos and it worked fine)

Run the Data Center Version of Repository Manager, create a new repository and set it up to download the updates for your machine.

Daniel Says this about the bundle OS selection: Select Linux. The operating system does not matter when you are updating outside of an operating system. It will only update firmware and BIOS, not drivers, outside of an OS. Selecting Linux will make it bootable and also keep it from downloading unnecessary drivers.

Follow his advice.

Now, select your bundle and click export. 

Follow the wizard and select to export it as SUU to a directory of your choice.

Let it download and export everthing and then copy the content of this folder into you empty FAT32 formatted USB stick.

Now you can boot your machine from the first stick we prepared, wait for SBUU to run, select