Cloned C: drive doesn't match original

I used Macrium Reflect to clone my C: drive onto another, identical, drive in onboard dock. My plan was to have a bootable copy of my system in case anything went wrong with updating to Win 10. The original has 32 folders and leaves 736 GB free on a 932-GB total. The clone has 7 files, and 893GB free.

Folders on the clone are:
MG
PerfLogs
Program Files
Program Files (x86)
Program Data
Users
Windows.

Many of my program and program (x86) files didn't make it over, so I guess the idea is to have a clean boot from the new drive. . . . so I think I've answered my own question about the difference.

But: Is there any way to save these old program files and feed them right back into my system if I resort to the new drive?

I was attempting to clone the entire drive, which has only one partition. The destination disk had stuff on it, but I understand that Macrium overwrites or deletes all that, and this certainly seems to be the case.

Here's my screenshot. I: should be a clone of C:

Try this image

D: is active by accident--it was originally the C: partition before I put C: on a separate drive.

I: is active because it was cloned from C:

Don't know if it's significant in this context, but I switched over to Win 10 last night.

I haven't had the chance to try it. The object was to have a usable Win 7 backup in case Win 10 gave me problems. I suyspect it does--from what I can see it's a full clean version of the oS, and nothing else. I had hoped to have my full old program environment.