I am going to be running my mill and lathe from the same computer but not at the same time. Are the keyboard inputs saved in the profile and seperate from other profiles? My mill and lathe inputs need to be different and want to be sure when i setup the lathe tomorrow i'm not changing all the work i did setting up the mill.

Is this M3 or M4?  And what do you mean by "keyboard inputs"?

I use M3 running on a Win10 mini-box PC with USB/UC100 motion controllers to control both my lathe and mill and they have quite separate profiles and I had no issues of one changing the other.

Key board inputs is a plugin for mach4 that allows you to use the keyboard to move the machine around using arrow keys and other functions. On the mill, moving z up and down the page up and down. On the lathe moving z uses right and left arrow. I have the mill setup now. If I setup the lathe to use the right and left arrows and go back to the mill the arrow keys control Z or the page up and down. Is that part of the machine setup saved in the profile?