Repackaging and redeployment is not a developer issue and really doesn't belong here. Such issues are more appropriate for someplace like ServerFault.
It is one thing to have lost all of the source code of an application, but even worse in some ways to have lost the deployment package. Sadly some shops fail to archive either of these.
However it was also common enough for shops to see RAD tools like VB6, Delphi, PowerBuilder, etc. as things to shove off on the worst of the worst of their developers. These poor slobs seldom got official Microsoft training that should have emphasized the importance of creating proper installers. For that matter even those courses tended to marginalize the topic. It doesn't help that the Web is full of "Mort teaching Mort" half-baked development even today, or that the pioneers who wrote many of the early serious VB programming books tended to be loose cannons and contrarians who didn't really believe deployment was a serious concern.
The end result is that lots of shops have machines with VB6 programs shoehorned onto them in a half-baked way. Often when deadlines loomed they let Old Mort install VB6 right onto the production server and let him hack away right there! So it's no wonder people get into trouble once a server needs to be replaced or its OS updated.
Those REG files with .000, .001, etc. extensions aren't anything normal that I'm aware of. For all I know they've fallen out of REGMON runs or some 3rd party packaging tool. Manual registry exports created using REGEDIT would normally have .REG extensions.
If you are actually "supporting" this application it implies that you have the source code, VB6 compiler, developer install packages for any 3rd party controls, and a writeup describing any special packaging and installation requirements (target machine DCOM/COM+ configuration, system requirements such as IIS or MSMQ or 3rd party DBMS Providers and Drivers, special folder requirements, software firewall rules, etc.).
From those it ought to be possible to compile a clean new copy of the EXE, DLLs, etc. and create a clean deployment package - even if some configuration still needs to be done manually before and after running the installer.
Without those you are a computer janitor and your question belongs over at ServerFault. It is no fun, I know. I've had to take part in such janitorial services myself all too often.