I recently got my slim jtagged with the reset glitch and the drive is not flashed.
Meaning all my disc backups are not working, just showing up as DVD video.
Can I make ISOs from those backup discs and then ftp them over?

Or is there another app I can run on the 360 that can still copy them?

if you dont have the iso's, I think you can still just use imgburn to get the iso back off the disk, then run iso2god and convert it over to god files, then ftp those to the console. I haven't tried this with games newer than 4th wave, but I know 4th wave games can be extracted from the burned disks with imgburn.