Hi Debra,
I'm not sure what exactly you mean by file? Do you mean the Directory? If so, that's not an issue and it can get quite large. Mine is already close to 2GB in size as I have lots of big PDF files. As Calibre uses a database to store the metadata and other info and keeps the books themselves in subdirectories, there shouldn't be too big a problem. Also, if you're using a newer Windows version such as XP, Vista, or 7 with NTFS (should be a default option if you're not sure what it is) then you shouldn't worry how big your directory gets or how many books you have.
As to wanting separate libraries, I'd recommend against it and use the tags feature instead. It's really easy to use whatever tags you want and then search the database for those tags, multiple tags, or even books that don't have that tag. Much easier to manage than multiple libraries.
This multi library issue pops up pretty regularly and everyone always recommends against it as it just adds unneeded complexity.
"Use the tags, Debra!"
Don't worry about how many books you have in the library, Calibre can handle a lot more.
Please make sure you back up you're Calibre directory (where the books and database are stored) to an external hard drive or CD/DVD since you can lose it all if you have problems! You can buy a couple inexpensive external USB hard drives and just copy the library directly to the device. Easy!
Hope this helps!
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