I go to install it move the resources, just fine, then after installing installer (tco, I have an nspire cx). It gets about half way through and then this message pops up on my calc:
Ndless successfully updated!

The device will not reboot.

*Always* keep 'ndless/ndless_resources.tns'.

then after hitting ok it restarts, and there is no file.

Seeing as it says Ndless was updated, it indicates that Ndless was installed correctly before.
(also I'm guessing it said it "will now reboot"?)

Did you follow the directions here?  ndless_resources should have been sent before sending the tno if I'm understanding this correctly.
It's just reminding you to not delete it, it doesn't create it.

1) The resources is still there
2)I did mean now, I am sorry
3)the file that isn't there is the installer I just assumed it would stay in my files, unless it is supposed to dissapear
4)Is there a way to see if it is on there?

The installer should not appear on your calc. Just try to launch some Ndless program to see if it installed properly