Hello idodis, welcome to the forum.
When you 'batch copy' photos from your source to the iPad, you are doing this via the iTunes synch? If so, you need to create new folders in your source file. For example, if you used a folder titled: FileA, this FileA will have a similar folder on the iPad. However, if you batch from source back into the same file on the iPad, you will wipe out all those files already there and replace with new.
So the solution is, at your source create a FileB and then when you sync, FileB will appear as FileB on your iPad. I hope this helps you.