Copying files to back them up, but losing some files, how to stop this?

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I tried to back up software, but I noticed that even though some of the files yellow folders copied over their particular contents weren't inside! For example- software, videos etc- Why is this?

Also, what does merge mean? =

I often get -"do you want to merge this file?"

Often when copying the same file name over the same file name I always click yes copy and replace. "When asks do you want to copy and replace." Is this the right thing to do?

My screensaver was set on 0 mins, would this affect copying? e.g. if I leave room etc and not on computer?
 
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Also, what does merge mean? =

Usually you get this message when you are wanting to add data to the registry. Basically it just means adding to it.
My screensaver was set on 0 mins, would this affect copying? e.g. if I leave room etc and not on computer?

No.
Often when copying the same file name over the same file name I always click yes copy and replace. "When asks do you want to copy and replace." Is this the right thing to do?

As long as you want the new file to replace the old existing file yes.
I tried to back up software, but I noticed that even though some of the files yellow folders copied over their particular contents weren't inside! For example- software, videos etc- Why is this?

If this is user data folder then it should have copied over but if this is an installed program you have trying to copy over to a new drive, you can't do that. The program would have to be reinstalled from installation media.
 
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