I have never done anything even remotely similar to what you are recounting, but I do have knowledge about filing extension and drop box etc. I checked the US embassy website from Nepal and stumbled upon this info which matches to what you are saying the reason for them being ineligible.
....Interview eligibility questions
On my previous visa, I did not apply for an extension of stay (using form I-539);
So like you said, it looks like since they filed the extension, that is making them ineligible to file for a waiver. Now technically they have to appear in person to renew the visa, but since now it is pandemic time bla bla, and they want to come visit you etc. You can make your case like you listed above about how they never overstayed for so many times and just filed for one extension for a serious reason etc. and take a chance if they give you a waiver. I did not really find any specific email as such, but instead find this 'contact us' page with different ways to stay in touch with them via chat, email, phone etc. with embassy personals. You may have known these routes already and I may be just repeating to you what you have known already, but that is all I could find in this case.
My two cents over here is they do not like people on visitor visa filing for extension as it might inadvertently show the inclination for immigrating which should not be the intent of this kind of visas, but we all know what is going on in here, but in paper and intentions, our actions should show those vibes. See in those questions I saw another one asking if the person in visitor visa has ever filed for TPS, those who did in the past would never get this waiver obviously as the person on that issued visa is misusing the intent for whatever reasons.
So in your case, I would say it is a tough call, but I would not discourage you from trying and emailing them, and here is the link to see all the various ways you can contact them.
PS. Just to let you know, I have emailed people in embassy in Nepal some years ago for some reason, they do respond back but do not expect them to be very elaborate and friendly either, they might even just repeat whatever is there on the site. They may not sound personal at all like here we may be, the reason, they are dealing with 100s of problems like this etc. and a lot of times, they have to be careful with their responses.
Last edited: 13-Jul-21 12:47 AM