I think it might be helpful if you indicated what distro of Linux you are referring to, since any meaningful answer to your question would depend on it. In any case, if you have installed Linux and it is working, then clearly nothing essential to the OS resides on either of those extra disks. Most likely they just contain other useful companion software (office suites, multimedia tools, etc) or documentation.
If you are certain that these disks contain software that is essential to your needs, then you could either just reinstall Linux and include that new software now that you've got the disks, or copy the programs you need from the CD then manually install them. -- J.W.