After hours of messing about trying to figure out a way to fix a file without resorting to windows i finally managed it. I had tried the GUI utils first but it just got to me and I gave up on them.
How i got an arm7 fix working in ubuntu linux and wine
I used the Arm7_fix.zip for this, and wine of course.
Not sure if it makes a difference but at the moment I also have mono for windows installed on my wine.
I tried to make a nice bash file, but alas it as having none of it (i am rubbish at these things and amazed i got it working) so if your going to do it then your either going to have to wait, or write one yourself as it is so simple to cut and paste I can not really be bothered that much, but i have left it as it is incase anyone wants to pick it up and finish it off. There are some other lines to the original bat file which would be nice if someone could put them back in, but this is the bits you need. i left the remove and make dirs in because it felt cleaner. Anyway, read the readme files in the original arm7_fix.zip it explains everything else.
I have put a # at the start of each line, this should help you in cut-n-pasting..obviously your going to have to remove the #'s as with it in place nothing much will happen. Your also going to have to make sure you are in the actual arm7_fix folder too using terminal and cd commands as things could get a bit messy if you just start firing off these commands anywhere but once there, with your donar and patient files in place, cuttng and pasting these lines should do the trick.
Many Many thanks to Bad-Ad84, CougRAWR and Go185, I would not have had a clue without you.
#rm -rf DONOR_UNPACK
#rm -rf PATIENT_UNPACK
#mkdir DONOR_UNPACK
#mkdir PATIENT_UNPACK
#wine ndstool -v -x ./donor/*.nds -7 DONOR_UNPACK/arm7.bin
#wine ndstool -v -x ./patient/*.nds -9 ./PATIENT_UNPACK/arm9.bin -y9 PATIENT_UNPACK/y9.bin -y7 PATIENT_UNPACK/y7.bin -d PATIENT_UNPACK/data -y PATIENT_UNPACK/overlay -t PATIENT_UNPACK/banner.bin -h PATIENT_UNPACK/header.bin
#wine ndstool -c fixed.nds -9 PATIENT_UNPACK/arm9.bin -7 DONOR_UNPACK/arm7.bin -y9 PATIENT_UNPACK/y9.bin -y7 PATIENT_UNPACK/y7.bin -d PATIENT_UNPACK/data -y PATIENT_UNPACK/overlay -t PATIENT_UNPACK/banner.bin -h PATIENT_UNPACK/header.bin
#rm -rf DONOR_UNPACK
#rm -rf PATIENT_UNPACK
By the way, for Ben10, i used what i had on the computer which was "deal or no deal" the arm fix worked fine using it.
On a R4 btw.