I did the tutorials on making mods via the creation kit website. Somehow I deleted the data in the "aaaMarkers" bsa. Does this matter? If so where can I copy it to replace it?

You mean the aaaMarkers cell? That means you've deleted the markers inside in your mod, and yes, that is a problem.

You'll need to remove the edits through the "Details" window within the Data window.

The actual "aaaMarkers " is present in the Left part of the Cell View window but has nothing in the Editor ID on the right side of the Cell View window.

Well then you've accidentally deleted the contents, which will cause serious errors ingame if your mod is loaded. You'll need to remove the edits from your mod like I stated.

I mean the actual "aaaMarkers" that came with the game.

if you clean up the edit in the details window (you really only need to delete the aaamarkers cell edit) the original aaamarkers will be back to normal

in the future, never duplicate a cell to create a new one. instead go to the top menu, select World, and Cells. it will open a tear-away cell view window. right click in the list of cells and select New. this will let you create a new cell from scratch

You can only modify vanilla content from within a mod you've made.