We have an audit coming up in the next 6 weeks and we are seeing we have missed some ATP testing on some production days. We also missed some Environmental testings for a few months. I am afraid that these will be counted as majors on our audit. How can we fix this before our audit?
The seriousness of the issue is perhaps going to depend on the products / risk in the production area, how many were missed, etc. As your post is in the BRC Packaging section I'd assume that you're not doing some sort of high-risk chilled RTE food for which the consequences could be most severe, so that helps a bit!
You could ignore it, hope that the auditor doesn't look at those records, and cross your fingers. I wouldn't recommend it though 
In your position I'd be inclined to take ownership of it. Don't go out of your way to draw the auditors attention to it, but put everything you possibly can in place to ensure it is covered as well as possible if they do happen to review it while on site. Log it as an internal non-conformance, put in robust corrective action (you need to do this anyway...), build a file of data to show what implications there were etc - hopefully you can pull together copies of subsequent tests, product micro etc to show that it didn't cause a problem?
You want to close the non-conformance as soon as you can, so go through your root cause process, identify the preventative action(s) to take, implement them, sign it all off, and if possible also have evidence that the actions have worked and that this has been reviewed to verify that it is the case - e.g. completion of all testing on time between now and the audit date, reviewed by the issuer of the non-conformance as part of the final close-out.
No food / packaging sites are perfect, so IMO an issue like this is really all about showing that you've caught the error and you've really gone over and above to make sure it doesn't happen again, and taken any necessary actions to mitigate any risk it may have caused.
