Not sure what you are “auto generating” with… I usually start from one of my other projects, or a gitignore example online, and reason about all the parts inside it, and start from there. Like any other configuration change, after you make it, pay attention for a while to make sure it is what you want.
You can always clone the repo somewhere else to verify that the correct files are being tracked. Doing so to a brand-new computer is the acid test to make sure you can still build the project.
Not sure what that means… the .gitignore file is a file like any other file, a file that may need updating through the life of your project, such as whenever you … wait for it … need to ignore different sets of files! 
No… think of previous commits as having been etched in stone. Changes to previously-tracked files will also continue to need committing forever, until you git rm those files AND have the .gitignore set to ignore them. Only at that point will they go away from the auto-proposed commit sets.
In other words, the huge file blocking you from uploading to a free provider will remain there and will remain blocking you. You can strip old commits and files from git but it’s a long tedious annoying process. There’s google help but it’s still a lot of fiddling.
My personal recommendation would be to abandon this repository and keep it around for historical reference, then make a fresh empty repository (WITH a correctly-configured .gitignore!!) and commit all your work files from the original repo at once, and move forward from there.