Save as illustrator from artboards changes layer visibility

[lTIsdale17]

I have a document with several artboards. I want to save the artboards individually as ai and eps files. When I do this the file that is created has different layers visible than what was in the file I saved from. So on a file that has two parts of a logo on different layers, one layer is off. So I have to then open all the files, change the visibility and resave. Is there something I'm missing?  A preference or simple change? 

Thanks!

[Monika Gause]

Please show something.

And please tell usexactly how you save the files.

[lTIsdale17]

I've attached screenshots of the original file with the different artboars, one of the layers and the one of the file that is created. The "shield" layer that was on originally is now off. I did a "save as", Illustrator, then checked the save each artboard to a seperate file option.