Is using rsync need to stop the demon?

I m using a rsync shell script in order to separate my working space to the owncloud synchronize data.
It was going fine for a while but now I m facing weird issue like irrelevant message about insufficient space and file conflict (some file are not uploaded instead there are renamed and a old version is dl from the server)

So : Is it a good pratice to stop the owncloud demon when running this rsync shell ?

Because I m using a paying version ( I was able to open a ticket, I will let you know if they found something.