Yes, it is possible for one to get a denial if the evidence requested is not submitted on time. But there are also exceptions to the rule, where you missed the deadline for reasons that were outside of your control.
Also, you made a request for a duplicate copy, which helps to avoid such a denial on this basis. And this should be on your record. Also, when you did eventually file the RFE, you gave an explanation that should over you.
Even if this does not work out easily, it is possible to rescue things. The best thing you can do is contact the USCIS and speak with a Tier 2 specialist. Explain everything to him/her and they will create a record of communication. That will be helpful in this case.
I know these issues can be confusing. If you want to discuss this or anything else by phone, I can send you an offer for that. There will be an additional fee, if you want to do that. Please let me know and I will send you the offer.
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