How to recover some backed up files to their locations?

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Recently I lost everything on my computer due to a hard drive error. I managed to recover, what I at the time thought, was all of my data through a data recovery application (Data Rescue). A few weeks later, after I had added many new files, I discovered that quite a number of old files had in fact not beed recovered (the files were there but were only 0 bytes in size).

Now luckily I had backed up my user folder on a separate drive before my computer crashed. But here is my question: how do I quickly replace all my 0 bytes files with the corresponding “full” ones from my backup drive?
 
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iPad Pro 12.9 latest iOS
What application did you use to back up your files to that separate drive ?

Cheers ... McBie
 

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