We appealed an editor's decision and sent a revised version, but he hasn't acknowledged it since 5 weeks

Question

This is about a post-review rejection. This is one of the top journals in our field. The reviewers found our work interesting but sent a long list of controls and additional experiments to do. The editor rejected it, saying it would take a lot of time. However, most of the concerns were addressable and we appealed. The editor said he'd be happy to reconsider and we can submit, via email, a point-by-point response letter along with a new version of the manuscript incorporating all the changes.

We took the time to do so and sent everything he asked us for via email, but there's been no response in 5 weeks. There's been no acknowledgment that he received it. My advisor sent a follow-up a week ago just to make sure he received the email, but there's been no response to that either. The portal doesn't show any indication of a reconsideration. The editor doesn't have any automated response indicating he is on a vacation, and according to the journal website, he doesn't seem to have moved to another job.

I know that the situation is unusual (especially with the emailing part), but what are my options? Should I reach out to someone above him? Resubmit the manuscript on the portal? (Which is what we probably would have in the first place if he didn't explicitly instruct us to email him the files)

I have never had this long of a waiting period before we heard back from the editor about whether they are sending my submission to reviewers. (Usually takes 2-3 weeks for me). But this time I don't even have an acknowledgment of the submission in 5 weeks.

Answer 1

I'm reading the OP as you sent the revised manuscript to the editor via email. If so, this is not a good idea - papers should be submitted via the journal's editorial management system (EMS). If you send a manuscript via email, the editor would have to submit it to the EMS for you. It's not that hard to do, but it's still annoying, especially if one is not a full-time staff of the journal.

However, this doesn't explain why the editor has not answered you for five weeks.

The best thing to do would be to keep contacting the journal until someone responds. Personally, I'd prefer contacting the journal office. Full-time staff of the journal ought to know what to do, or who to contact.

You could also just resubmit the manuscript. A properly-configured EMS will flag your manuscript as a duplicate (since it has already been submitted before), and then whoever is looking at the manuscript will in all likelihood assign it to the editor who originally handled the paper. Still not ideal (since it might be viewed as rather impertinent), but if your communication with the editor was via the EMS, those messages will be logged and can probably be accessed by a third party, and they should know what to do.

Answer 2

Here is an answer based on my comments:

1. Contact journal's editor-in-chief, describe the situation (very politely, without assigning any blame) and ask for an advice on how to proceed. Make sure, you include the current editor in the correspondence.

2. Given your username, I assume that you are still a graduate student. Then, make sure that you involve your graduate advisor in the process, maybe make them co-sign the email to the editor-in-chief. Also, ask your advisor if they happen to personally know the current editor and editor-in-chief. The knowledge of their personalities might alter the cause of action.

3. Regarding your question "I am worried that the current Editor might consider this as going over his head and be rejected as a result." - I can only say that it is impossible to predict, but given that the current editor did not respond to your emails for 5 weeks, going to the next level is appropriate.