Why don't you transfer your ROMs over the network to the new SD card ? You should be able to access your ROMs on the USB from your PC, just copy them to \\retropie\roms\<system> and that's all. See the docs page on transferring ROMs. For the missing icons - re-install the retropiemenu package, it probably stored its artwork on the USB drive.

wow, you guys are really in love with your usb sticks, defending them with life and limbs ... @dankcushions so what you are saying is that usbmount reliable mounts on every boot or that it is easier for a newcommer to linux to edit fstab than just transfer roms over network? @pjft if you edit fstab it will obviusly mount perfectly on each boot, but imo you cannot rely on everyone to know or understand how to edit fstab. tbh i doubt that there is really much of a diffrence today in speed, cost or reliability using a brand new usb stick vs sdcard considdering it is most likely using somewhat same chips and it is therefore up to the sdcard reader vs the controller on the usb stick which could arguably be marginally better on a usb stick than the raspberry, considdering it might be newer/better. however, considdering that it will be using usb 2.0, i doubt there will be a major diffrence if any anyway. a really high end sd card will most likely outperform a low end usb stick and vice versa,, high end sd card and high end usb sticks will most likely perform somewhat the same at about same price range, so in my oppinion it is just easier to just use a decent sd card and not have the hassle of editing anything (more than neccessary). however i do agree and see your point, that it might be easier for a windows user to have a drive you can actually read in windows. but considdering i dont use windows it isnt really a problem for me personally as i can just pop in the sd card in my computer and read it.

Thanks for confirming that, Worked a treat! :) (and apologies for bumping the thread. I won't touch it again I promise)

@koogelpotato Are the files listed when you ssh/SFTP to the snes rom directory on the pi? If so, check if they are all the accepted file extensions. If you've confirmed the files are indeed on the USB drive, you may want to check your freespace on the pi with df -h to see if you are out of space on the SD card.

@kaptainsteve No, however you need to restart ES in order to get the ROMs to show up once the transfer is complete.

@jonnykesh I meant @rbaker. The TO got it right IMO, talking about transferring ROMs to the USB drive and linking to the right docs for that.

@BuZz I'l have to look on the USB stick I use to house ROMs - barely ever plug it back into my PC unless I change some of the games. I build so many of these (because it's fun...well sometimes, when things go smoothly ;) and I'm constantly striving for the best performance from these little $5 computers, and I have GRANDIOSE dreams of having a master USB stick I put into any Pi, and it copies over EVERYTHING (ROMs, all scaper data/images, ALL my setting/config files), then just reboot and I have a brand new setup...but I don't think it's there quite yet. ROMS are WAY too big (like 14gb for me - and that's just 16 bit and below and a couple DOSBox games) so I'm still stuck using a USB stick to transfer.