My manuscript is rejected by the editor after receiving the reviewer's comments. The rejection is based on the comments from the reviewers. Two reviewers rated my manuscript as important. I received a full 2-page long comment from reviewer 2, which after all recommends re-submission after extensive revision. The problem is that one of my data is not relevant to the rest of the manuscript. So the manuscript needs extensive re-write, re-collect of the irrelevant data. The rest is ok. This is the reason for the rejection from the editor. So if I revise and re-collect the data, should I re-submit it to the same journal with a rebuttal letter?
Unless you were told not to resubmit then a complete reworking of the paper (from the data up) could be submitted. It might be rejected immediately, of course.
But I caution you about a "rebuttal". If you try to explain why they were wrong to reject the paper it will probably fail. If you, instead, submit a note of changes, updates, and improvements of the paper it will be better received. Unfortunately the word "rebuttal" is often misused in this context and the literal meaning gives the wrong impression about what should be included. If you think you need to explain why the editor was wrong, you should save yourself some time, effort, and pain and jut submit the paper (with improvements) elsewhere.
But note that "reject" means different things to different journals. Sometimes it is absolute and final (i.e. "go away"). Otherwise it just might mean "you've got a lot of work to do here - more than we care to deal with". Hopefully the rejection note from the editor lets you distinguish which situation applies.
Unless there's a specific note that they don't want a resubmission, reject usually just means you have to revise and resubmit. If you think the comments are all reasonable you're better off resubmitting to the same reviewers with an updated manuscript and a response letter.
I'm pretty sure it's because they'll list the initial submission date as whenever you resubmit. I can't recall the last paper that I had that didn't get "rejected" on the initial round of review.