Question: I plan to backup my large HDDs by rsync, and anticipate that it takes a few days. Is it safe to use the original HDD (adding files) while rsync is working? Or it is better to leave the HDDs untouched until the rsync is finished?
Answer: As others have already pointed out, it is safe to read from the source disk, or use the target disk outside out the target directory, while rsync is running. It is also safe to read within the target directory, especially if the target directory is being populated exclusively by the rsync run.
What’s not generally safe is to write within the source directory while rsync is running. “Writes” is anything that modifies the content of the source directory or any subdirectory thereof, so includes file updates, deletes, creation, etc.
Doing so won’t actually break anything, but the change may or may not actually get picked up by rsync for copying to the target location. That depends on the type of change, whether rsync has scanned that particular directory yet, and whether rsync has copied the file or directory in question yet.
However, there is an easy way around that: Once it finishes, run rsync again, with the same parameters. (Unless you have some funky delete parameter; if you do, then be a bit more careful.) Doing so will cause it to re-scan the source, and transfer any differences that weren’t picked up during the original run.
The second run should transfer only differences that happened during the previous rsync run, and as such will complete much faster. Thus, you can feel free to use the computer normally during the first run, but should avoid as much as possible making any changes to the source during the second run. If you can, strongly consider remounting the source file system read-only before starting the second rsync run. (Something like mount -o ro,remount /media/source should do.)