Sounds like you're missing a whole lot more than just the eq2.ini file then (see attached image for what my Everquest2 directory looks like)!
If you're missing as many files as you appear to be, missing the eq2.ini file is the least of your worries.
My suggestion is to uninstall and reinstall the game, as (if I'm understanding you correctly) you are missing a lot of key files. Then once that is done, try running the eq2map updater again, and see if it creates the eq2.ini file like it should.