I realise the question is confusing, so allow me to elaborate. I apologise for the phrasing, as I wasn't sure how to put it.
Here's the scenario: As my backup, currently my Mac launches Rsync every 12 hours to copy data from an external hard drive to another external hard drive. I like this backup method as a workaround to mirror the data in both sides without having to do RAID. I do not use the Rsync version that comes with the OS, but rather I got the latest one using the Homebrew tool for OS X.
The problem is I want to reinstall Yosemite from scratch, and these hard drives (there's more than one hard drive copying to another hard drive - I have various drives, each with their respective "clone" drive to have nice data redundancy) contain a lot of data and are encrypted with VeraCrypt, and the initial backup took a pretty long time for each. We are talking about 500 GB - 1TB drives.
So what will happen once I put the hard drives and their "mirrors" in the new setup? Will I have to start using Rsync from scratch or will Rsync know that I have used it with another setup before and continue the "mirroring" from there, considering that the hard drives will be exactly the same ones as before?