I just made a back-up copy of my Indesign file to my computers' hard drive from the external drive, and I noticed that whatever changes I made to one file was also made to the other file simultaneously. Why is this happening? Is it b/c of some sort of "cloud" connection?
You should give us more information:
Elaborate a little bit what you have done.
it sounds like you have an alias or shortcut of the file, not the actual file duplicated.