I have network of couple file sharing servers, but (there is always but

The thing is that I have around 2TB of data on that servers so I decided to transfer all files using rsync which is more automated and faster (correct me if i'm wrong). My question is if it's possible to somehow add those files to that server I mean something like moving those files in uploads directory and then changing server id of those files directly into the database. I've done this couple of times but on blank servers with no uploaded files on them but now i'm concerned that I might lose some data because on the old server that I want to transfer i have folders like 00000,00001 etc. and the same folders on the second one.
The scary part is that will it works if i just move the files in the right directories is there any chance of collision of encrypted filenames and is it going to be some problem with max_files limit per directory in linux.
Thanks