Sync production with Git

I am new to github,

Earlier we used to manually upload files on the production through FTP although git was present on the production. Due to this now git status shows many modified and untrack files.

To sync that with git we have downloaded all files from production and committed to git. Now git has all files same as production.

We have not pulled on production since last 6 months and because of this it shows modified and untracked files.

Now if we pull on the production there any 100% chances of the conflict happened on all modified files. As there are hundreds of modified files since last since month. Git pull will show conflict to all those files. In that case site will get down and we can not afford this.

We want a way to seamlessly sync production and Git.

Can anybody please help me on this?

Thanks in advance..!!

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