If I understand this, you want to extract only the SQLite file from a zip file which may contain any number of other file types, operate on the SQLite DB, and then discard the SQLite DB you operated on (but not from the zip file). One question I would ask is whether or not the SQLite files conform to some sort of naming convention such as a common file name extension. If so, then using something as simple as Archive::Zip to extract the SQLite DB, as it has a simple interface to grab hold of the names of the members and even some searching using membersMatching( { regex => $regex } ).

I think that if disk space is an issue, then memory would be and issue also. Are the SQLite files that big? Being that you only have to extract the SQLite DB file and have complete control over where it goes, it should be pretty easy to identify, extract, operate on and then delete that single file. (But maybe I am missing the point?)