The only thing I moved from my C: drive to E: were my Documents, Music, and Pictures folders. That might have caused a problem if I wqs using Windows Backup but I don't and it hasn't been a problem for me when using Macrium Reflect and FFS.
I had a look at the Free File Sync site, and the amount of praise heaped upon it is impressive. How do you use it with Macrium ? Mount image / Restore select folders with Free File Sync ?
Just for fun, jumping from the FFS site I found
this discussion, which tends to say you can't verify the integrity of a file after it's copied, and what do you mean by "verify", anyway ? Not that I understood the finer points of it, but it's the sort of thing that makes you think what the hell, let's copy the lot and be done with it.
Strictly speaking, I do not use Macrium Reflect (MR) with FFS. Both are used independently. I use MR to image my C: drive to back it up. Imaging is the only practical way to back up System (OS) files. However, imaging is very inefficient for backing up most data files. It takes too long and requires much too much storage space.
I keep my data segregated from my System. When I set up my desktop machine, I dragged my Documents, Music, and Pictures folders from my User folder on the C: drive (a 128GB Samsung 840 SSD) to my E: drive (a 2TB WD Black HDD). I have yet to mount an image since there is nothing there that I need to get at separately.
To back up my data on the E: drive (and the F: drive, another 2TB WD Black HDD), I use FFS and save the backup on 2TB WD Green HDDs that I use as external HDDs (I have a 3.5" HDD dock built into my computer). Normally, it is bad practice to save backups (in this case, images) on a drive that is installed in the machine being backed up but, since I backup my E: drive separately, I save my images to the E: drive to make restoring an image more convenient. The images get becked up whe the E: drive gets backed up.
FFS, when set to Mirror Mode, essentially makes a copy of the drive onto another drive. When updating the backup, FFS will compare the source drive to the backup drive to see what has changed, then will copy and paste changed and added files from the source drive to the backup drive and delete files on the backup drive that are no longer on the source drive.
I also have a Versioning drive (a 4TB WD Black HDD) in my machine. FFS has a feature, called Versioning, that will save data that gets deleted from a backup drive to a designated Versioning folder or drive. Versioning allows you to recover data that was deleted during a backup or earlier versions of changed files.
Another thing I use FFS for is to automatically backup my Favorites folder on my C: drive. I save the backup to a folder on the E: drive, which then gets backed up when the E: drive gets backed up. I also need to back up my App Data folder the same way but I haven't gotten around to setting it up (yet).
The FFS Verify hack I mentioned isn't officially sanctioned because it apparently caused problems on some systems but I haven't any problems with it. "Verify" means the program will check the file that was just copied to make sure the copy is identical to the original file.
Macrium Reflect has a similar function, only here it is sanctioned, where it will verify that an image just created doesn't have any errors in it.