UPDATE: Completely SOLVED as of post 16.
This question is for those who know about the folder/file structure of book entries and their relationship to database integrity. I'm trying something and would like to know if there is some impact unknown to me.
I've found a way to use Calibre to manage my hardcopy audiobooks and not just as a reference entry (and I love it). I know the various ways of getting files into Calibre's management. I know the author/title/filename structure it creates on all those methods.
My challenge is that these methods take a LONG time given the file size of audiobooks and zip files in this case. Copying such large files takes a lot of time and makes it inefficient. Calibre works by copying and creating a folder structure or copying and renaming in to the standard filename structure. Again, in this case it takes a long time per book.
Is there some unforseen impact of having files in the contain folders that do not follow the Calibre naming structure yet still show Calibre and manage as normal? I did some various tests learning some interesting things. I'll not go into every detail. The end result is that I tried 2 basic methods of "moving" files rather than letting the computer work to copy which is, of course, much less time when on the same hard drive.
1) I went directly to the Calibre book storage folder, moved the file into it, and renamed the file to match the Calibre structure of the existing epub copy.
Name - Author.epub
Name - Author.rar (my moved and renamed file - NOT imported)
2) I did as in #1 but DID NOT RENAME the file. From other testing experience, I didn't think it would read the file....
HOWEVER, in order to get Calibre to read the presence of these files which it normally would not do, I did a database rebuild. THIS WORKED!!!
The moved files were read as entries in the database and formats showed up as well as resulting preference rules activated base on those formats. A library check showed NO problems in the database or further file check.
The only 2 odd things were these:
1) The files that I renamed all created thumbnail files that showed up as DB entires in the Calibre formats even if the files were .rar files. These DB formats are easily deleted in a batch.
2) The file that I moved into an existing entry folder and DID NOT RENAME was the same rar file. It reads like anything else, not DB file was created, and the file name remained as the original. THIS IS THE SURPRISE. I thought Calibre couldn't read a file that doesn't follow the standard naming structure.
THIS IS WHERE I NEED INPUT from those in the know. I have restarted and had no issues in this test library. I open the containing folder and see the file still there with the original name. It reads like anything else. A library check shows no problems.
I want to use this last method of simply moving files, not worrying about renaming, then rebuilding the database. The copy speed is not longer a factor then. I'm aware of ensuring data prefs backups.
Is there some unforseen impact of having files in the contain folders that do not follow the Calibre naming structure yet still show Calibre and manage as normal? 
Thanks.