Again I appreciate everyone's feedback and interest. I am going to try to answer as many questions as I can that have been asked. But I only saw the Amiga for about an hour and a half today. A lot of what I saw meant little to me until now in retrospect. Our original main goal was simply to help devise a new database query filter. However, the 'issue' was raised that no one knew how to format floppies. We didn't expect to botch such an easy task and thus took little notice or precaution of anything seemingly outside of this small simple task. Actually our error was mostly in the fact that we somewhat dyslexically saw DH as HD...like high density. Anyway, the rest is history.
You said all the data was backed up weekly? To what? Using what? On the Amiga, while you can use a dedicated backup program, creating backups really is as simple as copying files to another device and then copying them back if the need arises.
The backups are done directly to the hard drive. There are actually two backup drawers named BU1 and BU2. There appears to be both files and at least some applications within these. But like I said before, the names were very generic to us so we couldn't tell files from apps except obvious ones like Calculator. The way I am figuring it is that if calculator was in a backup, what wouldn't be.
Outside the fact that the two staff members who use the Amiga know very little about the Amiga except for following routine steps, the man who set up their system clearly knew what he was doing and had been doing so for quite some time.
BTW, I do not know his name. But if they allow me to, I will post it back here tomorrow.
As for their backup application...after reading this forum, I am assuming that it was Quarterback since that was present on the system's UI (is that Workbench?) I didn't take much notice of it, or others named like it, since it was a name that seemed to have little to do with any procedure. But we both recall seeing Quarterback both on the system itself and on floppies elsewhere in the building.
Do you have access to the backed up files? It sounds like they're elsewhere on the hard drive.
That is correct. We only found during the last minutes the "show all" option. We found the upper menu on the UI by accident...holding a right-click. But the number of files that we saw within one of the backup drawers was pretty small...perhaps 25 at the most. Some of the backups are dated, however...like fileABC2001, fileABC2002, etc. Yet, the size of the partition we hosed was only 39.6 megs. So, perhaps we're still ok.
Can you describe the now-missing Main icon? Was it a white rectangular box with a little checkmark in it? That indicates a hard drive partition. Amiga drives can be accessed by either their device name or their volume name.
I wish I could describe it. There was just no reason to really take full visual inventory at the time when it was present. But the one staff member said it was more of a graphical icon...like a custom icon from a manufacturer. She said it looked like 'that one' where that one was a mnufacturer icon. But honestly, I recall it as a pretty simple white box. BTW, this was an Amiga 3000..not sure if there was a T after 3000 or not.
It sounds like you formatted device DH2: which had the volume name of Main.
That is my feeling as well. Compared to what I've seen as far as Amiga UI screenshots tonight on the Web, the Main thing seemed like the Work drawer / directory I've seen. Just a gut feeling based on a whole slew of things I can't really explain without the right Amiga terms.
Did anything else disappear from the desktop (we call it Workbench)? Those were probably files or programs on DH2: that had been "left out" for faster access. Formatting their home caused them to disappear.
There were definitely other items previously on the desktop that are no longer there. But not many. I'd guess at 5 being the most but I'm thinking it's really like 2-3. One I know of for certain was DH0?

that I first took to be a query of some sort. So, that one and Main make two. At most there were three other items. But I strongly feel it was more like 1 if any.
It's also possible that Main was a drawer somewhere on DH2: that had been left out, in which case we still need to discover what volume name DH2: corresponded to.
Understood. I really think Main was volume. Again I am basing this on little true knowledge except the fact that the setup seemed very organized yet simple. Outside of the obvious remaining utility icons, they are all task related and named accordingly.
I know I've left a few questions unanswered. But I will do my best to answer everything after I've had another look.
Oh...the other machine...as I understand it, it is a clone that existed as a backup machine. Apparently it was updated periodically. The last time it was updated was shortly before the man passed away which was about 3 months ago.
To me this would mean that the apps are all accessible. Since the data is most certainly backed up to machine #1's hard drive, we're only going to miss a couple of days worth of data. But according to staff members, such a thing would be very problematic. But who wouldn't say that?
The thing that concerns me along these lines is that when we've tried to open a few of the backup files, an error was presented that said something like \main\xyz could not be found. This leads me to believe that:
A) there are database queries where paths are hardcoded
B) the directory structure of the hosed partition will have to be exactly recreated.
Is it possible to do something as simple as copying DH2 from Amiga #2 to Amiga #1?
If so, from there we'd only have to copy back the backup files, right?
I'd prefer to exhaust all recovery methods first. More clearly, I'd like to not get into another situation where we have to say 'if only I would have tried that before this method which now makes that impossible'. Then again, we're kind of already in that position, aren't we.
Thanks again everyone.