In DTPO I used to index files instead of storing them into the internal database. Now in version 2 I reconized that DT stores files in their original format. So I think it’s no longer necessary to index files. What do you think: is it save enough to keep all my files in the internal DT structure? Can I delete the original files?
I keep my databases self-contained (Import-captures), and often move them from one computer to another, so I usually delete files from the Finder after they are imported to a database.
But I’ll occasionally Index-capture a file, such as large images, to hold down database size. If I subsequently move that database and not the external image (which usually resides in my Pictures folder), the Path to the image will break. But for my work that’s not very serious. If necessary, I can trace back to an image should I need it. If it is really useful, I’ll probably end up Importing it.
My databases have been stable for years; I don’t lose stuff.
But I’m also devoted to backups. I use Time Machine. I use Scripts > Export > Backup Archive. If I’ve invested time and effort in a database, I don’t wait for a scheduled backup, I initiate it when I take a break.
And I keep my computer and operating system in good shape. I avoid hacks (things that modify the operating system, such as Input Manager plugins, etc.)
Yeah, I don’t figure DTP can screw up the original files (at least, it can’t screw them up any more often than OS X could by itself). Just be a dear and backup frequently 
Yes it’s safe to keep the files in the DT database. They’re still “whole” in the database in 2.0; they’re copied into DT’s folder. So you can always either export them. or manually grub around in the database package and extract them.