When saving data do you overwrite or re save??

The question is a bit strange but it was the only way I knew how to ask it. I googled this but the term overwrite is used in another context.

Anyway like most people I save data off my computer on to external sources (eg I use Shadow Protect) which I find great.

But I also like to backup to a cute little 64gb flashdrive to carry with me.

What I would like some feedback on is whether you guys delete the files on the flashdrive and re copy from scratch or just re copy (i.e. overwritew) and any files/docs that are added or deleted are updated.

I stopped doing it this way years ago as I found it did not seem to work (i.e. adding the new files/docs and omitting the deleted ones). basically I couldn't trust it.

The problem is it takes sooooo long to delete and then re copy, I would love to just overwrite and any changes would be actioned.

How do others do this task???
I also use a program SyncBack,best thing since sliced bread.

One problem with overwrite is,JPEG photos lose a little bit of quality every time you resave them.:(