just out of curiosity, can you list the original games you have?
For preservation and copy-protected disks using pasti is the number one method. I know of no write-back software, maybe you should ask ijor directly.
I think I've read somewhere that is is possible to write back using a catweasle. About the discovery I don't know.
About the dumping process: Sometimes msa doesn't work when pasti works. I'm wondering if it would be best to first dump in pasti and then convert it to msa.
This way you have both, good preservation and 1:1 copies for playing them on your machines.
What you could do, is using one of ppera's HDD enabled games and just put them on your HDD http://ppera.07x.net/atari/fromhd.php
or use a flash drive floppy emulator with pasti images.
But before you waste a lot of time imaging everything you have, just visit http://www.atarimania.com
. And when you found some of your treasures there, it would be fantastic if you gave something back i.e. dump one or two games they don't have yet or scan a box,a disk or a manual they don't have. Every bit helps and every scan/dump people here can do helps saving money for getting another game.